Source: https://github.com/markziemann/GeneNameErrors2020

View the reports: http://ziemann-lab.net/public/gene_name_errors/

Intro

Gene name errors result when data are imported improperly into MS Excel and other spreadsheet programs (Zeeberg et al, 2004). Certain gene names like MARCH3, SEPT2 and DEC1 are converted into date format. These errors are surprisingly common in supplementary data files in the field of genomics (Ziemann et al, 2016). This could be considered a small error because it only affects a small number of genes, however it is symptomtic of poor data processing methods. The purpose of this script is to identify gene name errors present in supplementary files of PubMed Central articles in the previous month.

library("XML")
library("jsonlite")
library("xml2")
library("reutils")
library("readxl")
library("RCurl")

Get PMC IDs

Here I will be getting PubMed Central IDs for the previous month.

Start with figuring out the date to search PubMed Central.

CURRENT_MONTH=format(Sys.time(), "%m")
CURRENT_YEAR=format(Sys.time(), "%Y")

if (CURRENT_MONTH == "01") {
  PREV_YEAR=as.character(as.numeric(format(Sys.time(), "%Y"))-1)
  PREV_MONTH="12"
} else {
  PREV_YEAR=CURRENT_YEAR
  PREV_MONTH=as.character(as.numeric(format(Sys.time(), "%m"))-1)
}

DATE=paste(PREV_YEAR,"/",PREV_MONTH,sep="")
DATE
## [1] "2023/5"

Let’s see how many PMC IDs we have in the past month.

QUERY ='((genom*[Abstract]))'

ESEARCH_RES <- esearch(term=QUERY, db = "pmc", rettype = "uilist", retmode = "xml", retstart = 0, 
  retmax = 5000000, usehistory = TRUE, webenv = NULL, querykey = NULL, sort = NULL, field = NULL, 
  datetype = NULL, reldate = NULL, 
  mindate = paste(DATE,"/1",sep="") , maxdate = paste(DATE,"/31",sep=""))

pmc <- efetch(ESEARCH_RES,retmode="text",rettype="uilist",outfile="pmcids.txt")
## Retrieving UIDs 1 to 500
## Retrieving UIDs 501 to 1000
## Retrieving UIDs 1001 to 1500
## Retrieving UIDs 1501 to 2000
## Retrieving UIDs 2001 to 2500
## Retrieving UIDs 2501 to 3000
pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES
## [1] 2996
writeLines(pmc,con="pmc.txt")

Run the screen

Now run the bash script. Note that false positives can occur (~1.5%) and these results have not been verified by a human.

Here are some definitions:

  • NUM_XLS = Number of supplementary Excel files in this set of PMC articles.

  • NUM_XLS_ARTICLES = Number of articles matching the PubMed Central search which have supplementary Excel files.

  • GENELISTS = The gene lists found in the Excel files. Each Excel file is counted once even it has multiple gene lists.

  • NUM_GENELISTS = The number of Excel files with gene lists.

  • NUM_GENELIST_ARTICLES = The number of PMC articles with supplementary Excel gene lists.

  • ERROR_GENELISTS = Files suspected to contain gene name errors. The dates and five-digit numbers indicate transmogrified gene names.

  • NUM_ERROR_GENELISTS = Number of Excel gene lists with errors.

  • NUM_ERROR_GENELIST_ARTICLES = Number of articles with supplementary Excel gene name errors.

  • ERROR_PROPORTION = This is the proportion of articles with Excel gene lists that have errors.

system("./gene_names.sh pmc.txt")
results <- readLines("results.txt")

XLS <- results[grep("XLS",results,ignore.case=TRUE)]
NUM_XLS = length(XLS)
NUM_XLS
## [1] 4715
NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES
## [1] 1078
GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS

NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS
## [1] 504
NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES
## [1] 291
ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS

NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS
## [1] 161
GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES
##  [1] "PMC10225086" "PMC10218407" "PMC10216680" "PMC10214836" "PMC10226651"
##  [6] "PMC10225930" "PMC10217816" "PMC10216487" "PMC10214295" "PMC10210621"
## [11] "PMC10210411" "PMC10209733" "PMC10209063" "PMC10206494" "PMC10206047"
## [16] "PMC10203873" "PMC10203443" "PMC10203276" "PMC10202655" "PMC10200853"
## [21] "PMC10199912" "PMC10191432" "PMC10191288" "PMC10185564" "PMC10185556"
## [26] "PMC10181825" "PMC10164992" "PMC10156726" "PMC10151398" "PMC10150886"
## [31] "PMC10150505" "PMC10150242" "PMC10150019" "PMC10208567" "PMC10206066"
## [36] "PMC10203218" "PMC10199099" "PMC10194222" "PMC10188588" "PMC10188112"
## [41] "PMC10183592" "PMC10183018" "PMC10179737" "PMC10174503" "PMC10174322"
## [46] "PMC10174054" "PMC10170458" "PMC10171335" "PMC10170761" "PMC10170086"
## [51] "PMC10169700" "PMC10167087" "PMC10160042" "PMC10158796" "PMC10157938"
## [56] "PMC10156747" "PMC10154557" "PMC10150489"
NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES) 
NUM_ERROR_GENELIST_ARTICLES
## [1] 58
ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION
## [1] 0.1993127

Look at the errors detected

Here you can have a look at all the gene lists detected in the past month, as well as those with errors. The dates are obvious errors, these are commonly dates in September, March, December and October. The five-digit numbers represent dates as they are encoded in the Excel internal format. The five digit number is the number of days since 1900. If you were to take these numbers and put them into Excel and format the cells as dates, then these will also mostly map to dates in September, March, December and October.

#GENELISTS

ERROR_GENELISTS
##   [1] "PMC10225086 PMC_DL/PMC10225086/supplementaryfiles/13071_2023_5785_MOESM3_ESM.xlsx Celegans 2 44836 44624"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
##   [2] "PMC10225086 PMC_DL/PMC10225086/supplementaryfiles/13071_2023_5785_MOESM3_ESM.xlsx Celegans 2 44626 44621"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
##   [3] "PMC10225086 PMC_DL/PMC10225086/supplementaryfiles/13071_2023_5785_MOESM3_ESM.xlsx Celegans 2 44626 44623"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
##   [4] "PMC10218407 zip/Supplemental_Table_1_DEGs_v2.xlsx Drerio 18 45201 45184 44987 44992 44993 45172 45175 44992 44994 45179 45171 45173 44989 44996 44991 44992 44990 45181"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##   [5] "PMC10218407 zip/Supplemental_Table_1_DEGs_v2.xlsx Drerio 18 44992 45179 45184 45181 44993 45172 45171 45175 44987 45201 44992 44992 44991 44990 44994 44989 45173 44996"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##   [6] "PMC10218407 zip/Supplemental_Table_1_DEGs_v2.xlsx Drerio 18 45184 44992 45179 45181 45175 45171 45172 44993 44991 45201 44990 44994 44989 44992 45173 44996 44987 44992"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##   [7] "PMC10218407 zip/Supplemental_Table_1_DEGs_v2.xlsx Drerio 18 45175 45201 44996 45184 44994 44993 44989 44992 44992 44992 45173 45181 44991 45171 44987 45172 45179 44990"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##   [8] "PMC10218407 zip/Supplemental_Table_3_DEGs_v3.xlsx Drerio 18 45201 45184 44987 44992 44993 45172 45175 44992 44994 45179 45171 45173 44989 44996 44991 44992 44990 45181"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##   [9] "PMC10218407 zip/Supplemental_Table_3_DEGs_v3.xlsx Drerio 18 44992 45179 45184 45181 44993 45172 45171 45175 44987 45201 44992 44992 44991 44990 44994 44989 45173 44996"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##  [10] "PMC10218407 zip/Supplemental_Table_3_DEGs_v3.xlsx Drerio 18 45184 44992 45179 45181 45175 45171 45172 44993 44991 45201 44990 44994 44989 44992 45173 44996 44987 44992"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##  [11] "PMC10218407 zip/Supplemental_Table_3_DEGs_v3.xlsx Drerio 18 45175 45201 44996 45184 44994 44993 44989 44992 44992 44992 45173 45181 44991 45171 44987 45172 45179 44990"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##  [12] "PMC10216680 zip/Supplement_Tables.xlsx Hsapiens 1 44623"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##  [13] "PMC10214836 PMC_DL/PMC10214836/supplementaryfiles/Table_1.xlsx Hsapiens 1 45261"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##  [14] "PMC10226651 PMC_DL/PMC10226651/supplementaryfiles/Table_2.xlsx Hsapiens 5 44444 44446 44443 44261 44442"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##  [15] "PMC10225930 PMC_DL/PMC10225930/supplementaryfiles/mmc3.xlsx Hsapiens 3 37316 37316 37500"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
##  [16] "PMC10225930 PMC_DL/PMC10225930/supplementaryfiles/mmc3.xlsx Hsapiens 7 38961 37316 37500 40057 42248 39326 39142"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [17] "PMC10217816 zip/genes-2253974-supplementary/Telomere_dkd_Supp_Tables_2023_revised.xlsx Ggallus 1 40787"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
##  [18] "PMC10216487 zip/Supplemental_Table_S4_combined_gene_hit_list.xlsx Hsapiens 26 44989 45178 45261 44986 44987 44986 44995 44996 44987 44988 44990 44991 44992 44993 44994 45170 45179 45180 45181 45183 45171 45172 45173 45174 45175 45177"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [19] "PMC10214295 PMC_DL/PMC10214295/supplementaryfiles/mmc4.xlsx Hsapiens 3 44814 44627 44811"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
##  [20] "PMC10210621 zip/Supplemental-Tables_TCAI-revised.xlsx Hsapiens 1 43357"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
##  [21] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 12 12-Sep 2-Mar 4-Sep 3-Sep 10-Mar 2-Mar 9-Mar 2-Sep 8-Sep 5-Mar 10-Sep 11-Mar"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [22] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 5 10-Mar 2-Mar 8-Sep 4-Sep 3-Sep"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
##  [23] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 8 2-Sep 3-Sep 10-Mar 5-Mar 2-Mar 8-Sep 11-Mar 10-Sep"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##  [24] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 10 8-Mar 3-Sep 4-Mar 2-Sep 1-Sep 12-Sep 5-Mar 7-Mar 11-Mar 10-Mar"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
##  [25] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 3 2-Sep 8-Sep 11-Sep"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##  [26] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 12 8-Mar 3-Sep 7-Mar 1-Sep 12-Sep 11-Mar 2-Mar 2-Sep 5-Mar 10-Mar 4-Mar 11-Sep"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [27] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 1 1-Mar"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
##  [28] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 3 4-Sep 6-Sep 10-Mar"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##  [29] "PMC10210411 PMC_DL/PMC10210411/supplementaryfiles/13058_2023_1627_MOESM5_ESM.xlsx Hsapiens 5 1-Mar 6-Sep 2-Mar 1-Mar 12-Sep"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
##  [30] "PMC10209733 zip/TableS4.xlsx Hsapiens 3 44622 44626 44813"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [31] "PMC10209733 zip/TableS7.xlsx Hsapiens 10 44622 44813 44626 44812 44810 44813 44812 44626 44810 44810"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
##  [32] "PMC10209063 PMC_DL/PMC10209063/supplementaryfiles/41467_2023_38785_MOESM4_ESM.xlsx Drerio 14 44836 44814 44624 44819 44810 44621 44621 44622 44625 44629 44807 44631 30363 30417"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [33] "PMC10209063 PMC_DL/PMC10209063/supplementaryfiles/41467_2023_38785_MOESM4_ESM.xlsx Hsapiens 11 44621 44631 44814 44628 44626 44810 44621 44622 44625 44624 44809"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [34] "PMC10209063 PMC_DL/PMC10209063/supplementaryfiles/41467_2023_38785_MOESM4_ESM.xlsx Drerio 14 44621 44814 44836 44819 44810 44624 30363 44807 44622 30417 44631 44629 44621 44625"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [35] "PMC10209063 PMC_DL/PMC10209063/supplementaryfiles/41467_2023_38785_MOESM4_ESM.xlsx Hsapiens 11 44621 44814 44810 44626 44624 44631 44622 44809 44621 44625 44628"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [36] "PMC10209063 PMC_DL/PMC10209063/supplementaryfiles/41467_2023_38785_MOESM4_ESM.xlsx Drerio 14 44624 44807 44629 44810 44819 44814 44836 44621 30417 44631 44625 44621 30363 44622"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [37] "PMC10209063 PMC_DL/PMC10209063/supplementaryfiles/41467_2023_38785_MOESM4_ESM.xlsx Hsapiens 11 44810 44624 44621 44809 44814 44625 44626 44631 44621 44628 44622"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [38] "PMC10209063 PMC_DL/PMC10209063/supplementaryfiles/41467_2023_38785_MOESM6_ESM.xlsx Hsapiens 14 45174 44986 44986 45174 44996 44987 45175 44993 44992 44991 41701 45173 45179 45172"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
##  [39] "PMC10206494 PMC_DL/PMC10206494/supplementaryfiles/mmc2.xlsx Hsapiens 12 44811 44806 44623 44814 44623 44626 44813 44623 44623 44621 44623 44815"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##  [40] "PMC10206047 PMC_DL/PMC10206047/supplementaryfiles/Table7.XLSX Hsapiens 1 44990"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
##  [41] "PMC10203873 PMC_DL/PMC10203873/supplementaryfiles/Table_4.xlsx Hsapiens 2 44819 44621"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
##  [42] "PMC10203443 PMC_DL/PMC10203443/supplementaryfiles/mmc4.xls Athaliana 2 44835 44778"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
##  [43] "PMC10203443 PMC_DL/PMC10203443/supplementaryfiles/mmc4.xls Athaliana 1 44835"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
##  [44] "PMC10203276 PMC_DL/PMC10203276/supplementaryfiles/mmc17.xlsx Hsapiens 5 44625 44627 44626 44629 44628"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
##  [45] "PMC10202655 PMC_DL/PMC10202655/supplementaryfiles/mmc3.xlsx Hsapiens 81 39873 37316 37135 37226 37316 39873 38231 37316 38412 37135 40057 39508 41883 36951 41153 41153 41883 39142 38961 39326 40787 36951 38961 38777 39692 40422 40238 38777 39142 41153 38596 40422 38047 36951 38231 39326 38047 36951 39142 39326 37865 40057 40787 37500 37316 39873 40787 37865 37681 40238 40422 40057 40603 40603 39508 38596 37865 37500 37681 37681 38777 39692 38412 38412 37226 37135 39508 39692 37316 38047 37316 38961 38231 38596 40603 37226 36951 41883 36951 40238 37500"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
##  [46] "PMC10202655 PMC_DL/PMC10202655/supplementaryfiles/mmc3.xlsx Hsapiens 27 37226 36951 37316 36951 40238 40603 37316 37681 38047 38412 38777 39142 39508 39873 37135 40422 40787 41153 41883 37500 37865 38231 38596 38961 39326 39692 40057"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [47] "PMC10200853 PMC_DL/PMC10200853/supplementaryfiles/mmc3.xlsx Hsapiens 27 44995 44996 45180 45178 44986 44987 45175 44988 45183 44994 45182 44989 45174 45181 45261 45170 45173 45179 44991 45184 45176 44990 44992 45171 45177 44993 45172"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [48] "PMC10199912 PMC_DL/PMC10199912/supplementaryfiles/41598_2023_35312_MOESM7_ESM.xlsx Hsapiens 6 37500 40057 36951 36951 37226 39326"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
##  [49] "PMC10191432 zip/adg2235_Data_file_S1.xlsx Hsapiens 28 36951 37226 38231 40422 39326 38777 38596 40787 41883 39508 37865 40603 38961 36951 37316 37500 39873 40238 37135 39142 42248 41153 39692 38047 40057 37681 37316 38412"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
##  [50] "PMC10191432 zip/adg2235_Data_file_S2.xlsx Hsapiens 28 40603 37135 39326 38777 40238 37681 41153 39508 39142 36951 37316 37226 36951 38961 39873 37500 40422 39692 38231 37865 41883 37316 38047 38412 40787 42248 38596 40057"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
##  [51] "PMC10191288 PMC_DL/PMC10191288/supplementaryfiles/pone.0283553.s007.xlsx Hsapiens 1 25419"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [52] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM7_ESM.xlsx Hsapiens 1 IRF5-Oct"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
##  [53] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM4_ESM.xlsx Hsapiens 9 44623 44623 44627 44806 44806 44806 44806 44806 44806"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
##  [54] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM4_ESM.xlsx Hsapiens 10 44807 44808 44622 44621 44621 44624 44622 44626 44815 44812"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
##  [55] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM4_ESM.xlsx Hsapiens 35 44807 44626 44622 44621 44811 44812 44815 44626 44815 44629 44629 44811 44811 44626 44621 44815 44819 44625 44625 44622 44819 44625 44812 44811 44626 44812 44812 44812 44815 44811 44622 44812 44626 44811 44625"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [56] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM6_ESM.xlsx Hsapiens 4 44625 44622 44621 44622"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
##  [57] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM6_ESM.xlsx Hsapiens 2 44622 44621"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [58] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM6_ESM.xlsx Hsapiens 25 44621 44622 44622 44625 44621 44621 44621 44626 44626 44626 44621 44626 44621 44625 44622 44621 44622 44622 44622 44626 44621 44624 44622 44626 44631"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
##  [59] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM6_ESM.xlsx Hsapiens 7 44626 44622 44631 44621 44621 44622 44624"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##  [60] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM6_ESM.xlsx Hsapiens 24 44621 44629 44626 44625 44626 44622 44621 44621 44621 44626 44626 44621 44622 44629 44625 44896 44626 44624 44626 44626 44626 44621 44631 44622"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
##  [61] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM6_ESM.xlsx Hsapiens 3 44622 44621 44631"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##  [62] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM6_ESM.xlsx Hsapiens 31 44625 44622 44621 44621 44621 44629 44621 44621 44626 44621 44621 44621 44622 44629 44621 44622 44626 44621 44626 44621 44622 44621 44621 44626 44626 44626 44626 44622 44625 44625 44621"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
##  [63] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM5_ESM.xlsx Hsapiens 6 44807 44621 44622 44819 44815 44626"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
##  [64] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM5_ESM.xlsx Hsapiens 107 44806 44621 44811 44811 44626 44626 44806 44814 44625 44813 44811 44627 44819 44819 44811 44626 44815 44628 44622 44622 44622 44811 44811 44811 44810 44810 44810 44810 44810 44627 44627 44627 44627 44815 44815 44815 44815 44815 44815 44815 44629 44626 44626 44626 44626 44812 44812 44812 44812 44812 44628 44806 44806 44806 44806 44806 44806 44623 44623 44819 44813 44813 44813 44813 44621 44814 44814 44814 44625 44808 44809 44807 44813 44813 44806 44627 44811 44815 44806 44819 44814 44814 44622 44622 44806 44819 44814 44625 44812 44813 44813 44621 44621 44627 44626 44626 44626 44806 44806 44806 44806 44806 44625 44622 44810 44815 44629"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
##  [65] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM5_ESM.xlsx Hsapiens 108 44811 44815 44806 44806 44625 44812 44623 44627 44626 44819 44625 44811 44623 44626 44815 44806 44813 44813 44813 44811 44627 44622 44622 44622 44811 44811 44811 44810 44810 44810 44810 44627 44627 44815 44815 44815 44815 44626 44626 44812 44812 44628 44806 44806 44819 44819 44813 44813 44813 44813 44813 44621 44621 44814 44814 44814 44814 44625 44808 44809 44807 44806 44814 44806 44819 44810 44622 44622 44811 44806 44815 44627 44627 44627 44626 44626 44626 44806 44814 44814 44626 44806 44626 44806 44806 44819 44811 44812 44621 44815 44625 44815 44810 44815 44629 44626 44812 44806 44806 44806 44806 44621 44622 44629 44812 44628 44813 44815"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
##  [66] "PMC10185564 PMC_DL/PMC10185564/supplementaryfiles/41467_2023_38140_MOESM5_ESM.xlsx Hsapiens 24 44807 44622 44811 44622 44621 44811 44819 44812 44819 44811 44815 44625 44819 44815 44625 44812 44812 44626 44819 44815 44815 44622 44626 44625"