Gene Name Error Monthly Dashboard
Mark Ziemann
2021-09-03
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")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] "2021/8"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 = DATE, maxdate = DATE)
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## Retrieving UIDs 3001 to 3500pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 3015writeLines(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] 4137NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 621GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 570NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 254ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 294GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC8357957" "PMC8357835" "PMC8357785" "PMC8386547" "PMC8366456"
## [6] "PMC8389471" "PMC8386078" "PMC8386026" "PMC8379442" "PMC8387103"
## [11] "PMC8386872" "PMC8386171" "PMC8384175" "PMC8384091" "PMC8383299"
## [16] "PMC8356190" "PMC8351575" "PMC8381363" "PMC8379831" "PMC8369001"
## [21] "PMC8362890" "PMC8378686" "PMC8346570" "PMC8346558" "PMC8371109"
## [26] "PMC8363664" "PMC8361094" "PMC8361032" "PMC8372368" "PMC8367384"
## [31] "PMC8370613" "PMC8369824" "PMC8361881" "PMC8361107" "PMC8359384"
## [36] "PMC8365341" "PMC8350897" "PMC8350412" "PMC8350206" "PMC8339674"
## [41] "PMC8363306" "PMC8363264" "PMC8362953" "PMC8352983" "PMC8325267"
## [46] "PMC8325244" "PMC8323604" "PMC8358448" "PMC8302675" "PMC8298472"
## [51] "PMC8357189" "PMC8355892" "PMC8355820" "PMC8355708" "PMC8355218"
## [56] "PMC8352595" "PMC8346669" "PMC8343164" "PMC8354477" "PMC8353793"
## [61] "PMC8353259" "PMC8352870" "PMC8351597" "PMC8333778" "PMC8326637"
## [66] "PMC8346036" "PMC8345867" "PMC8344067" "PMC8344058" "PMC8340308"
## [71] "PMC8333418" "PMC8295287" "PMC8336464" "PMC8335167" "PMC8321682"
## [76] "PMC8321653" "PMC8330917" "PMC8329287" "PMC8329071" "PMC8322386"
## [81] "PMC8316582" "PMC8316576" "PMC8316550" "PMC8316454" "PMC8327752"
## [86] "PMC8325265" "PMC8325178" "PMC8324785" "PMC8323712"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 89ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.3503937Look 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] "PMC8357957 /pmc/articles/PMC8357957/bin/41467_2021_25088_MOESM6_ESM.xlsx Mmusculus 3 44260 44261 44257"
## [2] "PMC8357835 /pmc/articles/PMC8357835/bin/41386_2021_1031_MOESM2_ESM.xlsx Mmusculus 9 44262 44442 44261 44264 44263 44443 44441 44447 44444"
## [3] "PMC8357835 /pmc/articles/PMC8357835/bin/41386_2021_1031_MOESM2_ESM.xlsx Mmusculus 4 44263 44261 44450 44262"
## [4] "PMC8357785 /pmc/articles/PMC8357785/bin/41386_2021_1023_MOESM6_ESM.xlsx Hsapiens 25 37865 40238 37681 38412 40422 41153 39692 39508 39873 37316 38047 36951 40787 37500 39326 40057 38231 40603 36951 38596 37226 39142 37135 38777 37316"
## [5] "PMC8386547 /pmc/articles/PMC8386547/bin/aging-13-203398-s002.xlsx Hsapiens 1 43525"
## [6] "PMC8366456 /pmc/articles/PMC8366456/bin/EMBR-22-e50193-s002.xlsx Hsapiens 10 42069 42253 42066 42252 42250 42251 42248 42067 42064 42064"
## [7] "PMC8389471 /pmc/articles/PMC8389471/bin/pgen.1009094.s027.xlsx Mmusculus 107 42985 42985 42985 42985 42800 42992 42985 42985 42989 42983 42984 42986 42805 42804 42795 42796 42989 42982 42982 42982 42988 42796 42993 42990 42986 42986 42979 42796 42795 42990 42804 42800 42802 42802 42802 42799 42795 42799 42799 42795 42795 42984 42796 42796 42981 42980 42980 42980 42988 42987 42987 42987 42798 42980 42992 42987 42801 42982 42803 42802 42984 42797 42984 42983 42984 42986 42805 42804 42795 42796 42989 42982 42982 42982 42988 42985 42796 42993 42990 42986 42986 42979 42796 42795 42990 42804 42800 42802 42802 42802 42799 42795 42799 42799 42795 42795 42984 42796 42796 42981 42980 42980 42980 42988 42987 42987 42987"
## [8] "PMC8389471 /pmc/articles/PMC8389471/bin/pgen.1009094.s028.xlsx Mmusculus 26 40603 40795 40794 40609 40787 40793 40607 40796 40800 40799 40797 40606 40788 40611 40605 40602 40612 40604 40786 40789 40610 40603 40792 40791 40602 40608"
## [9] "PMC8389471 /pmc/articles/PMC8389471/bin/pgen.1009094.s029.xlsx Mmusculus 61 42065 42257 42256 42071 42258 42249 42255 42069 42064 42258 42257 42258 42262 42255 42064 42261 42065 42254 42259 42072 42065 42068 42259 42250 42068 42250 42068 42065 42249 42069 42250 42070 42070 42253 42255 42073 42067 42064 42074 42066 42253 42066 42070 42068 42248 42073 42251 42072 42065 42253 42254 42253 42253 42253 42251 42064 42254 42253 42064 42070 42070"
## [10] "PMC8389471 /pmc/articles/PMC8389471/bin/pgen.1009094.s037.xlsx Mmusculus 8 41158 41158 40978 40970 40973 41158 41158 40974"
## [11] "PMC8386078 /pmc/articles/PMC8386078/bin/13059_2021_2466_MOESM5_ESM.xlsx Hsapiens 12 43892 44077 44077 44083 44080 44083 44083 44083 44077 44077 44077 44083"
## [12] "PMC8386078 /pmc/articles/PMC8386078/bin/13059_2021_2466_MOESM5_ESM.xlsx Hsapiens 6 43898 44079 44080 44083 44083 44083"
## [13] "PMC8386026 /pmc/articles/PMC8386026/bin/12915_2021_1108_MOESM14_ESM.xlsx Drerio 21 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786 40786"
## [14] "PMC8379442 /pmc/articles/PMC8379442/bin/mmc4.xlsx Mmusculus 1 14977"
## [15] "PMC8387103 /pmc/articles/PMC8387103/bin/Table_3.xlsx Hsapiens 25 44078 43898 44081 43891 44080 44075 43892 43891 44076 43892 44077 44084 43896 44083 43895 43893 43899 44082 43897 44085 43894 44166 44086 43900 44079"
## [16] "PMC8387103 /pmc/articles/PMC8387103/bin/Table_3.xlsx Hsapiens 25 44075 44081 44076 43891 43898 43896 44084 44085 44083 44082 43899 43895 44078 43892 43893 43892 43897 43891 44077 44080 43894 44166 44086 43900 44079"
## [17] "PMC8387103 /pmc/articles/PMC8387103/bin/Table_3.xlsx Hsapiens 25 43891 44075 44078 44076 44082 44085 43895 43896 43892 44084 44083 43899 44080 44081 43891 43892 43893 44077 43897 43898 43894 44166 44086 43900 44079"
## [18] "PMC8387103 /pmc/articles/PMC8387103/bin/Table_4.xlsx Hsapiens 25 44078 44075 43891 44081 44076 43898 43896 44085 44082 44084 44083 43895 43899 43892 44080 43892 43891 43893 44077 43897 43894 44166 44086 43900 44079"
## [19] "PMC8387103 /pmc/articles/PMC8387103/bin/Table_6.xlsx Hsapiens 1 44256"
## [20] "PMC8387103 /pmc/articles/PMC8387103/bin/Table_6.xlsx Hsapiens 1 44440"
## [21] "PMC8387103 /pmc/articles/PMC8387103/bin/Table_6.xlsx Hsapiens 2 44443 44446"
## [22] "PMC8386872 /pmc/articles/PMC8386872/bin/ppat.1009785.s019.xlsx Hsapiens 22 43899 44080 44085 43891 43898 43896 43891 44082 44076 44089 44084 43897 44075 44081 44083 44079 43895 43893 43892 44077 43892 44086"
## [23] "PMC8386872 /pmc/articles/PMC8386872/bin/ppat.1009785.s021.xlsx Hsapiens 40 44257 44256 44256 44256 44257 44256 44448 44262 44448 44450 44262 44448 44448 44262 44262 44448 44259 44265 44450 44261 44447 44262 44261 44448 44441 44448 44265 44450 44265 44448 44448 44448 44448 44448 44448 44448 44448 44450 44450 44448"
## [24] "PMC8386171 /pmc/articles/PMC8386171/bin/Data_Sheet_1.xlsx Hsapiens 5 44448 44449 44260 44531 44266"
## [25] "PMC8386171 /pmc/articles/PMC8386171/bin/Data_Sheet_1.xlsx Hsapiens 1 44443"
## [26] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 24 44531 44256 44257 44256 44265 44257 44258 44259 44260 44261 44262 44263 44264 44440 44449 44450 44451 44441 44442 44443 44445 44446 44447 44448"
## [27] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [28] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [29] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 2 44256 44450"
## [30] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 1 44451"
## [31] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 1 44441"
## [32] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 22 44531 44256 44257 44256 44257 44258 44259 44260 44261 44262 44263 44264 44440 44449 44450 44441 44442 44443 44445 44446 44447 44448"
## [33] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [34] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [35] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 2 44453 44531"
## [36] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 23 44531 44256 44257 44256 44265 44257 44258 44259 44260 44261 44262 44263 44264 44440 44449 44450 44441 44442 44443 44445 44446 44447 44448"
## [37] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [38] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [39] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 2 44256 44261"
## [40] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 3 44256 44454 44261"
## [41] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 4 44256 44257 44256 44441"
## [42] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 23 44531 44256 44257 44256 44265 44257 44258 44259 44260 44261 44262 44263 44264 44440 44449 44450 44441 44442 44443 44445 44446 44447 44448"
## [43] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [44] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [45] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 4 44256 44257 44257 44440"
## [46] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 3 44445 44266 44441"
## [47] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 3 44258 44264 44447"
## [48] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 23 44531 44256 44257 44256 44265 44257 44258 44259 44260 44261 44262 44263 44264 44440 44449 44450 44441 44442 44443 44445 44446 44447 44448"
## [49] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [50] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [51] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 1 44256"
## [52] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 2 44266 44444"
## [53] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 7 44256 44258 44259 44441 44444 44447 44448"
## [54] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [55] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [56] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 3 44075 43897 43896"
## [57] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 2 44445 44448"
## [58] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 2 44264 44441"
## [59] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [60] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [61] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 1 44079"
## [62] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 3 44443 44261 44450"
## [63] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 2 44259 44441"
## [64] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [65] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [66] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 3 44085 43896 43899"
## [67] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 2 44266 44453"
## [68] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [69] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [70] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 6 44075 44083 43899 44089 43896 43897"
## [71] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 5 44447 44263 44440 44453 44448"
## [72] "PMC8384175 /pmc/articles/PMC8384175/bin/pcbi.1009224.s006.xlsx Hsapiens 1 44531"
## [73] "PMC8384091 /pmc/articles/PMC8384091/bin/11427_2021_1990_MOESM2_ESM.xlsx Hsapiens 28 44451 44531 44266 44452 44256 44257 44265 44258 44259 44261 44262 44263 44264 44449 44453 44445 44446 44447 44448 44256 44257 44440 44443 44444 44260 44450 44442 44454"
## [74] "PMC8383299 /pmc/articles/PMC8383299/bin/Table_7.XLSX Hsapiens 4 37104 37469 37834 38200"
## [75] "PMC8383299 /pmc/articles/PMC8383299/bin/Table_7.XLSX Hsapiens 4 37104 37469 37834 38200"
## [76] "PMC8356190 /pmc/articles/PMC8356190/bin/jitc-2021-002467supp001.xlsx Hsapiens 1 43891"
## [77] "PMC8351575 /pmc/articles/PMC8351575/bin/peerj-09-11931-s005.xls Hsapiens 7 2021/03/02 2021/03/11 2021/09/14 2021/09/12 2021/09/04 2021/03/10 2021/09/03"
## [78] "PMC8381363 /pmc/articles/PMC8381363/bin/Data_Sheet_1.xlsx Hsapiens 25 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44440 44449 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [79] "PMC8379831 /pmc/articles/PMC8379831/bin/13148_2021_1152_MOESM2_ESM.xlsx Hsapiens 167 43900 44083 43893 44075 44083 43899 43898 44083 44083 44083 44083 43891 44083 44083 44083 44083 44083 44083 44083 43891 44083 44083 44083 43898 44083 44083 43891 44083 44083 44083 44083 43900 43891 44083 44083 44084 44083 43898 44083 44083 43894 43900 44083 44085 44089 44083 43891 44083 44083 43898 43891 44083 43892 43894 44077 43891 43898 43896 44082 43896 44088 44086 44075 43892 44082 43892 43893 44086 43894 43891 44079 44078 43891 44081 43891 44085 44084 44082 43901 44078 43891 43891 43901 43892 43896 44084 44082 44084 44082 44083 44078 43900 44083 44083 43897 43901 44078 43894 44083 44083 43901 44083 43891 44083 43900 44083 43900 44083 43891 44083 44082 43894 43899 44082 43891 44083 43894 44082 44083 44083 44084 44083 44083 43901 44082 44083 44083 44083 44078 44083 43896 44083 44085 44079 43901 44085 44083 44083 44083 43893 44083 44085 44082 44082 44083 44083 44083 44083 43894 44083 44083 44084 44083 44083 43900 44082 43894 43900 44083 44081 44083 44083 44082 43898 44082 44083 44083"
## [80] "PMC8369001 /pmc/articles/PMC8369001/bin/mmc2.xlsx Hsapiens 1 36951"
## [81] "PMC8369001 /pmc/articles/PMC8369001/bin/mmc2.xlsx Hsapiens 27 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 38231 40238 40057 37316 38596 37865 43714"
## [82] "PMC8362890 /pmc/articles/PMC8362890/bin/mmc6.xlsx Mmusculus 5 37104 37469 38200 37469 37834"
## [83] "PMC8378686 /pmc/articles/PMC8378686/bin/pgen.1009737.s010.xlsx Rnorvegicus 3 41153 36951 37316"
## [84] "PMC8378686 /pmc/articles/PMC8378686/bin/pgen.1009737.s011.xlsx Rnorvegicus 3 41153 36951 37316"
## [85] "PMC8378686 /pmc/articles/PMC8378686/bin/pgen.1009737.s014.xlsx Rnorvegicus 1 37316"
## [86] "PMC8346570 /pmc/articles/PMC8346570/bin/41467_2021_25012_MOESM3_ESM.xlsx Hsapiens 3 43900 43899 43897"
## [87] "PMC8346558 /pmc/articles/PMC8346558/bin/41467_2021_24967_MOESM3_ESM.xlsx Rnorvegicus 1 40238"
## [88] "PMC8346558 /pmc/articles/PMC8346558/bin/41467_2021_24967_MOESM3_ESM.xlsx Rnorvegicus 2 40238 40238"
## [89] "PMC8346558 /pmc/articles/PMC8346558/bin/41467_2021_24967_MOESM8_ESM.xlsx Rnorvegicus 27 40787 40057 41153 36951 39142 39326 40238 38231 39692 37865 37316 38777 39508 38047 38412 37135 37500 37681 40603 36951 38596 37316 41883 38961 39873 40422 42248"
## [90] "PMC8346558 /pmc/articles/PMC8346558/bin/41467_2021_24967_MOESM9_ESM.xlsx Rnorvegicus 27 40787 40057 41153 36951 39142 39326 40238 38231 39692 37865 37316 38777 39508 38047 38412 37135 37500 37681 40603 36951 38596 37316 41883 38961 39873 40422 42248"
## [91] "PMC8371109 /pmc/articles/PMC8371109/bin/41598_2021_95816_MOESM3_ESM.xlsx Hsapiens 1 ENSBTAG00000054263-NOVA1"
## [92] "PMC8363664 /pmc/articles/PMC8363664/bin/41467_2021_25215_MOESM4_ESM.xlsx Hsapiens 1 40057"
## [93] "PMC8363664 /pmc/articles/PMC8363664/bin/41467_2021_25215_MOESM4_ESM.xlsx Hsapiens 1 40057"
## [94] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 16 40057 40057 38961 40057 40057 38596 40057 40057 40057 40057 40057 38961 40057 38961 40057 38961"
## [95] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 13 40057 38961 38596 38596 40057 40057 38961 40057 40057 38961 38961 38961 40057"
## [96] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 19 40057 40057 38961 40057 38961 38596 38961 40057 40057 38961 38596 40057 40057 40057 40057 38596 40057 38961 38596"
## [97] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 6 40057 40057 38961 40057 40057 40057"
## [98] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 26 40057 38961 38961 40057 40057 40057 40057 40057 40057 40057 40057 38961 40057 40057 38596 40057 38961 38961 38961 40057 38961 38596 40057 38961 38961 38961"
## [99] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 19 40057 38961 38961 40057 38961 38961 38596 38961 40057 40057 38961 40057 40057 40057 38961 38961 40057 40057 38596"
## [100] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 22 40057 40057 38961 40057 38961 38596 40057 38961 40057 40057 38961 38961 38961 38961 40057 38961 38596 38961 38961 38961 40057 38961"
## [101] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 15 40057 40057 40057 40057 38596 38961 40057 38596 40057 40057 38596 40057 38961 38961 38961"
## [102] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 19 40057 38961 38961 40057 38961 38961 40057 40057 38961 40057 40057 40057 38596 40057 38961 38596 40057 40057 40057"
## [103] "PMC8361094 /pmc/articles/PMC8361094/bin/41525_2021_229_MOESM2_ESM.xlsx Hsapiens 20 40057 38961 40057 40057 38596 40057 38596 40057 40057 38961 38961 40057 38961 38596 40057 38961 38961 40057 40057 38961"
## [104] "PMC8361032 /pmc/articles/PMC8361032/bin/41467_2021_24951_MOESM9_ESM.xlsx Hsapiens 28 44454 44257 44256 44263 44260 44264 44451 44440 44443 44265 44448 44257 44449 44262 44259 44441 44444 44442 44450 44256 44261 44266 44258 44447 44446 44453 44531 44445"
## [105] "PMC8372368 /pmc/articles/PMC8372368/bin/Table_1.xlsx Hsapiens 4 44445 44450 44261 44449"
## [106] "PMC8372368 /pmc/articles/PMC8372368/bin/Table_1.xlsx Hsapiens 16 44442 44443 44446 44445 44262 44450 44264 44451 44261 44447 44441 44258 44440 44444 44449 44260"
## [107] "PMC8372368 /pmc/articles/PMC8372368/bin/Table_1.xlsx Hsapiens 17 44442 44443 44446 44445 44262 44450 44264 44451 44259 44261 44447 44441 44258 44440 44444 44449 44260"
## [108] "PMC8372368 /pmc/articles/PMC8372368/bin/Table_1.xlsx Hsapiens 17 44442 44443 44446 44445 44262 44450 44264 44451 44259 44261 44447 44441 44258 44440 44444 44449 44260"
## [109] "PMC8372368 /pmc/articles/PMC8372368/bin/Table_1.xlsx Hsapiens 16 44442 44443 44446 44445 44262 44450 44264 44451 44261 44447 44441 44258 44440 44444 44449 44260"
## [110] "PMC8372368 /pmc/articles/PMC8372368/bin/Table_1.xlsx Hsapiens 17 44442 44443 44446 44445 44262 44450 44264 44451 44259 44261 44447 44441 44258 44440 44444 44449 44260"
## [111] "PMC8372368 /pmc/articles/PMC8372368/bin/Table_1.xlsx Hsapiens 16 44442 44443 44446 44445 44262 44450 44264 44451 44261 44447 44441 44258 44440 44444 44449 44260"
## [112] "PMC8372368 /pmc/articles/PMC8372368/bin/Table_1.xlsx Hsapiens 16 44442 44443 44446 44445 44262 44450 44264 44451 44261 44447 44441 44258 44440 44444 44449 44260"
## [113] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-fig2-data1.xls Dmelanogaster 5 44444 44440 44444 44441 44443"
## [114] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-fig2-data1.xls Dmelanogaster 9 44444 44443 44444 44441 44444 44443 44441 44440 44444"
## [115] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table1-data1.xlsx Dmelanogaster 1 44078"
## [116] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table1-data1.xlsx Dmelanogaster 1 44078"
## [117] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table1-data1.xlsx Dmelanogaster 1 44078"
## [118] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table1-data1.xlsx Dmelanogaster 1 44443"
## [119] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table2-data1.xlsx Dmelanogaster 1 44444"
## [120] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table2-data1.xlsx Dmelanogaster 1 44443"
## [121] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table2-data1.xlsx Dmelanogaster 6 44444 44444 44441 44441 44440 44440"
## [122] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table2-data1.xlsx Dmelanogaster 1 44443"
## [123] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table2-data1.xlsx Dmelanogaster 1 44443"
## [124] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table2-data1.xlsx Dmelanogaster 1 44443"
## [125] "PMC8367384 /pmc/articles/PMC8367384/bin/elife-69937-table2-data1.xlsx Dmelanogaster 1 44441"
## [126] "PMC8370613 /pmc/articles/PMC8370613/bin/pbio.3001364.s029.xlsx Hsapiens 1 44256"
## [127] "PMC8370613 /pmc/articles/PMC8370613/bin/pbio.3001364.s030.xlsx Hsapiens 1 44256"
## [128] "PMC8369824 /pmc/articles/PMC8369824/bin/Table_1.xlsx Hsapiens 2 44450 44448"
## [129] "PMC8361881 /pmc/articles/PMC8361881/bin/13059_2021_2439_MOESM2_ESM.xlsx Hsapiens 7 39508 38412 37316 39142 37500 40057 40422"
## [130] "PMC8361107 /pmc/articles/PMC8361107/bin/41598_2021_95637_MOESM1_ESM.xlsx Hsapiens 9 44256 44263 44443 44256 44440 44262 44265 44454 44453"
## [131] "PMC8361107 /pmc/articles/PMC8361107/bin/41598_2021_95637_MOESM1_ESM.xlsx Hsapiens 2 43897 44088"
## [132] "PMC8361107 /pmc/articles/PMC8361107/bin/41598_2021_95637_MOESM2_ESM.xlsx Hsapiens 8 44265 44257 44448 44443 44262 44453 44256 44263"
## [133] "PMC8361107 /pmc/articles/PMC8361107/bin/41598_2021_95637_MOESM2_ESM.xlsx Hsapiens 10 44453 44448 44257 44265 44262 44256 44443 44440 44263 44256"
## [134] "PMC8359384 /pmc/articles/PMC8359384/bin/MEC-30-3645-s003.xlsx Ggallus 1 40057"
## [135] "PMC8365341 /pmc/articles/PMC8365341/bin/Data_Sheet_2.xlsx Hsapiens 7 44264 44448 44447 44258 44442 44444 44445"
## [136] "PMC8350897 /pmc/articles/PMC8350897/bin/EMMM-13-e12881-s002.xlsx Hsapiens 2 39326 37500"
## [137] "PMC8350897 /pmc/articles/PMC8350897/bin/EMMM-13-e12881-s004.xlsx Hsapiens 1 39508"
## [138] "PMC8350897 /pmc/articles/PMC8350897/bin/EMMM-13-e12881-s010.xlsx Hsapiens 2 37500 39326"
## [139] "PMC8350412 /pmc/articles/PMC8350412/bin/mmc2.xlsx Mmusculus 1 44085"
## [140] "PMC8350206 /pmc/articles/PMC8350206/bin/JCSM-12-1064-s004.xlsx Hsapiens 57 39508 40057 38047 39326 40057 36951 36951 40787 39326 38777 40057 40057 40057 40422 38047 40057 40057 40422 40057 40057 40057 40057 40057 36951 40057 39692 40057 40057 40057 40057 40057 40057 39692 38047 37500 37316 40057 40057 40057 38777 40057 39508 40422 40057 38777 40422 40787 37316 40057 40057 38412 40057 40057 40238 40238 40057 36951"
## [141] "PMC8350206 /pmc/articles/PMC8350206/bin/JCSM-12-1064-s004.xlsx Hsapiens 11 40057 40057 36951 38047 40057 40422 40057 40057 40057 38777 40057"
## [142] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s001.xlsx Mmusculus 129 43894 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 44084 43899 44078 43900 43900 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 43901 43901 43901 43901 43901 43901 43896 43896 43896 43896 43896 43896 44077 44077 44077 44079 43893 43893 43893 43895 43897 43897 43897 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44075 44075 44075 43891 43891 43891 44081 44081 44081 44081 44081 44081 44081 44081"
## [143] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s003.xlsx Mmusculus 4 43900 44083 44083 44083"
## [144] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s004.xlsx Mmusculus 4 44082 43898 44084 43893"
## [145] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s005.xlsx Mmusculus 3 44106 44108 44110"
## [146] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s005.xlsx Mmusculus 3 44106 44108 44108"
## [147] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s007.xlsx Mmusculus 97 43899 44084 44084 43900 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44082 44082 44082 44078 43896 43896 43896 43896 43896 43896 43896 44077 44079 44086 43892 43892 43892 43893 43893 43893 43895 43891 43891 43892 43892 43892 43892 43892 43892 43894 44076 44076 43897 43897 43897 43897 43897 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44075 44075 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44080 44080 44080 44080 44080 44080 44080 44080"
## [148] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s008.xlsx Mmusculus 97 43899 44084 44084 43900 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44082 44082 44082 44078 43896 43896 43896 43896 43896 43896 43896 44077 44079 44086 43892 43892 43892 43893 43893 43893 43895 43891 43891 43892 43892 43892 43892 43892 43892 43894 44076 44076 43897 43897 43897 43897 43897 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44075 44075 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44080 44080 44080 44080 44080 44080 44080 44080"
## [149] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s009.xlsx Mmusculus 1 44083"
## [150] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s010.xlsx Mmusculus 3 44106 44110 44108"
## [151] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s010.xlsx Mmusculus 3 44106 44108 44108"
## [152] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s012.xlsx Hsapiens 3 44110 44108 44106"
## [153] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s012.xlsx Hsapiens 3 44108 44108 44106"
## [154] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s013.xlsx Mmusculus 129 43894 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 44084 43899 44078 43900 43900 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 43901 43901 43901 43901 43901 43901 43896 43896 43896 43896 43896 43896 44077 44077 44077 44079 43893 43893 43893 43895 43897 43897 43897 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44085 44075 44075 44075 43891 43891 43891 44081 44081 44081 44081 44081 44081 44081 44081"
## [155] "PMC8339674 /pmc/articles/PMC8339674/bin/EMBR-22-e52716-s015.xlsx Mmusculus 4 44082 43898 44084 43893"
## [156] "PMC8363306 /pmc/articles/PMC8363306/bin/Table1.xls Hsapiens 1 2020/09/06"
## [157] "PMC8363264 /pmc/articles/PMC8363264/bin/Table_1.XLSX Hsapiens 80 44445 44445 44445 44445 44531 44453 44446 44446 44446 44266 44447 44447 44447 44447 44447 44447 44258 44261 44261 44261 44450 44256 44256 44442 44442 44444 44444 44441 44441 44441 44441 44441 44441 44259 44262 44262 44262 44262 44449 44449 44449 44257 44257 44257 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44265 44265 44265 44265 44443 44443 44443 44443 44443 44443 44443 44443 44443 44451 44451 44440 44264 44260 44263 44263 44263 44454 44454 44256 44257"
## [158] "PMC8362953 /pmc/articles/PMC8362953/bin/ppat.1009812.s010.xlsx Mmusculus 21 43168 43162 43348 43164 43167 43161 43351 43165 43161 43345 43166 43352 43350 43347 43353 43344 43354 43349 43160 43160 43346"
## [159] "PMC8352983 /pmc/articles/PMC8352983/bin/41392_2021_713_MOESM2_ESM.xlsx Hsapiens 28 43720 43529 43709 43535 43722 43527 43710 43525 43532 43534 43526 43533 43526 43716 43531 43530 43715 43800 43718 43713 43712 43723 43711 43719 43525 43528 43717 43714"
## [160] "PMC8352983 /pmc/articles/PMC8352983/bin/41392_2021_713_MOESM2_ESM.xlsx Hsapiens 14 43897 43898 43893 43891 43892 43895 43891 43896 43899 43900 43892 43894 44166 43901"
## [161] "PMC8352983 /pmc/articles/PMC8352983/bin/41392_2021_713_MOESM2_ESM.xlsx Ggallus 32 44084 44076 44088 43893 44088 43892 43895 44088 44075 44088 44088 43900 44088 44078 44088 44088 44088 44088 44088 44088 43900 44088 44088 44084 44076 44088 44088 44088 44088 44088 44088 44088"
## [162] "PMC8325267 /pmc/articles/PMC8325267/bin/pnas.2104758118.sd02.xlsx Hsapiens 4 43898 43899 44075 44083"
## [163] "PMC8325267 /pmc/articles/PMC8325267/bin/pnas.2104758118.sd02.xlsx Hsapiens 1 43895"
## [164] "PMC8325244 /pmc/articles/PMC8325244/bin/pnas.2102344118.sd02.xlsx Mmusculus 14 44446 44447 44449 44443 44442 44451 44260 44262 44256 44454 44264 44445 44448 44444"
## [165] "PMC8323604 /pmc/articles/PMC8323604/bin/peerj-09-11872-s001.xlsx Hsapiens 1 44076"
## [166] "PMC8358448 /pmc/articles/PMC8358448/bin/Table_1.XLSX Hsapiens 1 43716"
## [167] "PMC8358448 /pmc/articles/PMC8358448/bin/Table_1.XLSX Hsapiens 1 43719"
## [168] "PMC8358448 /pmc/articles/PMC8358448/bin/Table_1.XLSX Ggallus 1 43716"
## [169] "PMC8358448 /pmc/articles/PMC8358448/bin/Table_3.XLSX Hsapiens 5 43711 43525 43525 43717 43525"
## [170] "PMC8302675 /pmc/articles/PMC8302675/bin/41398_2021_1527_MOESM1_ESM.xlsx Hsapiens 1 40057"
## [171] "PMC8302675 /pmc/articles/PMC8302675/bin/41398_2021_1527_MOESM1_ESM.xlsx Hsapiens 1 40057"
## [172] "PMC8302675 /pmc/articles/PMC8302675/bin/41398_2021_1527_MOESM1_ESM.xlsx Hsapiens 2 36951 39508"
## [173] "PMC8302675 /pmc/articles/PMC8302675/bin/41398_2021_1527_MOESM1_ESM.xlsx Hsapiens 1 36951"
## [174] "PMC8302675 /pmc/articles/PMC8302675/bin/41398_2021_1527_MOESM1_ESM.xlsx Hsapiens 2 36951 39508"
## [175] "PMC8298472 /pmc/articles/PMC8298472/bin/42003_2021_2356_MOESM4_ESM.xlsx Hsapiens 3 43898 43892 44082"
## [176] "PMC8357189 /pmc/articles/PMC8357189/bin/NIHMS1726847-supplement-2.xlsx Mmusculus 8 43893 44081 44084 44085 43895 43897 43901 43896"
## [177] "PMC8355892 /pmc/articles/PMC8355892/bin/Table_1.xlsx Hsapiens 1 44448"
## [178] "PMC8355820 /pmc/articles/PMC8355820/bin/Table_1.xlsx Hsapiens 3 41699 41701 41886"
## [179] "PMC8355820 /pmc/articles/PMC8355820/bin/Table_2.xlsx Hsapiens 4 41699 41702 41707 41883"
## [180] "PMC8355820 /pmc/articles/PMC8355820/bin/Table_4.xlsx Hsapiens 5 41699 41700 41701 41707 41883"
## [181] "PMC8355708 /pmc/articles/PMC8355708/bin/Data_Sheet_1.xlsx Hsapiens 1 44263"
## [182] "PMC8355708 /pmc/articles/PMC8355708/bin/Data_Sheet_1.xlsx Hsapiens 1 44258"
## [183] "PMC8355708 /pmc/articles/PMC8355708/bin/Data_Sheet_1.xlsx Hsapiens 1 44258"
## [184] "PMC8355708 /pmc/articles/PMC8355708/bin/Data_Sheet_1.xlsx Hsapiens 1 44258"
## [185] "PMC8355708 /pmc/articles/PMC8355708/bin/Data_Sheet_1.xlsx Hsapiens 1 44263"
## [186] "PMC8355708 /pmc/articles/PMC8355708/bin/Data_Sheet_1.xlsx Hsapiens 1 44263"
## [187] "PMC8355218 /pmc/articles/PMC8355218/bin/41598_2021_95085_MOESM1_ESM.xlsx Athaliana 49 39661 37530 38261 37165 39661 37165 37895 14332 14332 14332 39295 38565 14331 38261 37316 14333 37165 39295 42248 38565 39356 38261 39661 37135 38930 38261 37104 37104 14312 37712 37469 39295 38200 39356 38261 37834 39661 38930 37530 38261 37712 36982 36982 14335 37347 38261 39661 39661 14336"
## [188] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig4-figsupp1-data1.xlsx Mmusculus 13 37500 38412 38596 38777 38961 39326 39692 40057 40422 40603 40787 41883 42248"
## [189] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig4-figsupp1-data1.xlsx Mmusculus 11 37500 38412 38596 38777 38961 39326 39692 40057 40422 40787 42248"
## [190] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig4-figsupp1-data1.xlsx Mmusculus 11 37500 38412 38596 38777 38961 39326 39692 40057 40422 40787 42248"
## [191] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig4-figsupp1-data1.xlsx Mmusculus 11 37500 38412 38596 38777 38961 39326 39692 40057 40422 40787 42248"
## [192] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig4-figsupp1-data1.xlsx Mmusculus 11 37500 38412 38596 38777 38961 39326 39692 40057 40422 40787 42248"
## [193] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig4-figsupp1-data1.xlsx Mmusculus 11 37500 38412 38596 38777 38961 39326 39692 40057 40422 40787 42248"
## [194] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig4-figsupp1-data1.xlsx Mmusculus 13 37500 38412 38596 38777 38961 39326 39692 40057 40422 40603 40787 41883 42248"
## [195] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig5-data1.xlsx Mmusculus 1 36951"
## [196] "PMC8352595 /pmc/articles/PMC8352595/bin/elife-65104-fig5-data3.xlsx Mmusculus 14 38777 40787 39508 39692 40057 39142 37316 39873 39326 40422 37316 38412 37681 37135"
## [197] "PMC8346669 /pmc/articles/PMC8346669/bin/mmc3.xlsx Mmusculus 5 36951 38777 36951 38777 37316"
## [198] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc10.xlsx Hsapiens 1 40787"
## [199] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc10.xlsx Hsapiens 1 40787"
## [200] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 2 37043 37316"
## [201] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 1 37316"
## [202] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 6 37043 37681 37408 37196 37561 11383"
## [203] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 2 37681 37681"
## [204] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 2 37043 37196"
## [205] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 4 37043 37408 37773 37196"
## [206] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 4 37043 37408 37773 38139"
## [207] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 4 37043 38231 37408 15220"
## [208] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc13.xlsx Hsapiens 2 38231 38231"
## [209] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc1.xlsx Hsapiens 3 40787 40787 40787"
## [210] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc2.xlsx Hsapiens 1 40787"
## [211] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc3.xlsx Hsapiens 6 40422 40057 40057 40787 40057 40057"
## [212] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc3.xlsx Hsapiens 11 40422 40057 40057 40787 40787 40787 40057 40057 40057 40057 40057"
## [213] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc3.xlsx Ggallus 6 37135 40057 39873 38047 40787 40057"
## [214] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc7.xlsx Hsapiens 2 40787 39326"
## [215] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc7.xlsx Hsapiens 2 40787 39326"
## [216] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc8.xlsx Hsapiens 22 37043 37408 37196 40787 37773 38139 39326 38504 38869 26177 26543 39234 37500 39600 37561 26908 39965 36951 40330 38961 40695 27273"
## [217] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc8.xlsx Hsapiens 10 40787 40787 39326 39326 39326 37500 39326 36951 38961 39326"
## [218] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc9.xlsx Hsapiens 26 40787 39326 37196 37561 37043 26177 37408 26543 37773 38139 40422 26908 27273 38504 38869 39234 27638 40057 39600 28004 37500 37316 39142 44440 38777 33482"
## [219] "PMC8343164 /pmc/articles/PMC8343164/bin/mmc9.xlsx Hsapiens 21 40787 39326 40787 39326 40787 39326 40422 40787 39326 39326 39326 40057 40422 39326 37500 37316 39142 37500 38777 40422 40057"
## [220] "PMC8354477 /pmc/articles/PMC8354477/bin/pgen.1009679.s015.xlsx Hsapiens 7 2002-03-01 2005-03-01 2012-09-01 2002-09-01 2003-09-01 2004-09-01 2008-09-01"
## [221] "PMC8354477 /pmc/articles/PMC8354477/bin/pgen.1009679.s017.xlsx Hsapiens 26 2001-12-01 2001-03-01 2002-03-01 2001-03-01 2010-03-01 2011-03-01 2002-03-01 2003-03-01 2004-03-01 2005-03-01 2006-03-01 2007-03-01 2008-03-01 2009-03-01 2015-09-01 2001-09-01 2010-09-01 2011-09-01 2002-09-01 2003-09-01 2004-09-01 2005-09-01 2006-09-01 2007-09-01 2008-09-01 2009-09-01"
## [222] "PMC8353793 /pmc/articles/PMC8353793/bin/13024_2021_475_MOESM13_ESM.xlsx Dmelanogaster 1 38231"
## [223] "PMC8353793 /pmc/articles/PMC8353793/bin/13024_2021_475_MOESM13_ESM.xlsx Dmelanogaster 1 38231"
## [224] "PMC8353259 /pmc/articles/PMC8353259/bin/Table_5.XLSX Hsapiens 5 44447 44450 44441 44261 44446"
## [225] "PMC8352870 /pmc/articles/PMC8352870/bin/41598_2021_95618_MOESM2_ESM.xlsx Ggallus 4 43800 43800 43800 43800"
## [226] "PMC8351597 /pmc/articles/PMC8351597/bin/Table_2.xlsx Hsapiens 16 2021-03-02 2021-03-09 2021-09-09 2021-09-12 2021-09-04 2021-09-08 2021-03-06 2021-09-02 2021-03-07 2021-09-06 2021-09-10 2021-12-01 2021-03-08 2021-03-01 2021-09-07 2021-09-11"
## [227] "PMC8351597 /pmc/articles/PMC8351597/bin/Table_2.xlsx Hsapiens 16 2021-03-02 2021-03-09 2021-09-09 2021-09-12 2021-09-06 2021-03-03 2021-09-08 2021-03-06 2021-09-02 2021-03-08 2021-12-01 2021-09-10 2021-03-07 2021-03-01 2021-09-11 2021-09-07"
## [228] "PMC8351597 /pmc/articles/PMC8351597/bin/Table_3.xlsx Hsapiens 3 2021-03-01 2021-09-07 2021-09-11"
## [229] "PMC8333778 /pmc/articles/PMC8333778/bin/MOL2-15-2046-s001.xlsx Hsapiens 28 41342 41341 41339 41343 41338 41340 41521 41338 41519 41338 41337 41529 41339 41520 41340 41338 41524 41522 41522 41341 41519 41520 41340 41529 41520 41519 41339 41520"
## [230] "PMC8326637 /pmc/articles/PMC8326637/bin/sj-xlsx-1-imr-10.1177_03000605211029521.xlsx Hsapiens 10 44262 44258 44531 44261 44256 44264 44263 44260 44259 44257"
## [231] "PMC8346036 /pmc/articles/PMC8346036/bin/Table_1.XLSX Hsapiens 41 44264 44446 44262 44446 44260 44261 44258 44449 44445 44442 44260 44257 44449 44444 44531 44441 44454 44257 44445 44441 44448 44443 44447 44256 44446 44257 44258 44442 44451 44259 44256 44531 44265 44261 44440 44448 44256 44453 44450 44441 44444"
## [232] "PMC8346036 /pmc/articles/PMC8346036/bin/Table_1.XLSX Hsapiens 27 44256 44445 44260 44447 44257 44256 44259 44263 44266 44261 44450 44440 44264 44443 44262 44453 44258 44449 44531 44441 44442 44448 44451 44265 44454 44446 44266"
## [233] "PMC8345867 /pmc/articles/PMC8345867/bin/pgen.1009684.s001.xls Hsapiens 1 44082"
## [234] "PMC8345867 /pmc/articles/PMC8345867/bin/pgen.1009684.s004.xls Hsapiens 6 44450 44450 44450 44257 44450 44263"
## [235] "PMC8345867 /pmc/articles/PMC8345867/bin/pgen.1009684.s006.xls Hsapiens 2 44256 44447"
## [236] "PMC8344067 /pmc/articles/PMC8344067/bin/NIHMS1722142-supplement-2.xlsx Dmelanogaster 5 43800 43709 43710 43713 43712"
## [237] "PMC8344067 /pmc/articles/PMC8344067/bin/NIHMS1722142-supplement-2.xlsx Dmelanogaster 5 44166 44075 44076 44079 44078"
## [238] "PMC8344067 /pmc/articles/PMC8344067/bin/NIHMS1722142-supplement-2.xlsx Dmelanogaster 2 43710 43713"
## [239] "PMC8344058 /pmc/articles/PMC8344058/bin/Table_1.XLSX Hsapiens 11 43161 43346 43347 43349 43344 43350 43163 43165 43358 43353 43164"
## [240] "PMC8340308 /pmc/articles/PMC8340308/bin/NIHMS1720095-supplement-2.xlsx Hsapiens 5 42256 42071 42066 42064 42065"
## [241] "PMC8333418 /pmc/articles/PMC8333418/bin/41598_2021_95051_MOESM1_ESM.xlsx Hsapiens 1 44261"
## [242] "PMC8295287 /pmc/articles/PMC8295287/bin/41419_2021_4000_MOESM4_ESM.xlsx Hsapiens 19 43712 43715 43531 43717 43526 43526 43711 43534 43528 43715 43533 43534 43717 43717 43717 43710 43716 43717 43529"
## [243] "PMC8295287 /pmc/articles/PMC8295287/bin/41419_2021_4000_MOESM4_ESM.xlsx Hsapiens 12 43712 43526 43529 43535 43531 43710 43719 43717 43532 43532 43717 43711"
## [244] "PMC8295287 /pmc/articles/PMC8295287/bin/41419_2021_4000_MOESM4_ESM.xlsx Hsapiens 2 43712 43715"
## [245] "PMC8295287 /pmc/articles/PMC8295287/bin/41419_2021_4000_MOESM4_ESM.xlsx Hsapiens 1 43717"
## [246] "PMC8336464 /pmc/articles/PMC8336464/bin/Table_3.xlsx Hsapiens 4 44266 44444 44444 44257"
## [247] "PMC8335167 /pmc/articles/PMC8335167/bin/Data_Sheet_1.xlsx Hsapiens 24 44531 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44446 44447 44448"
## [248] "PMC8335167 /pmc/articles/PMC8335167/bin/Data_Sheet_1.xlsx Hsapiens 26 44260 44443 44448 44451 44264 44450 44265 44256 44266 44440 44453 44263 44259 44262 44257 44531 44454 44449 44256 44447 44446 44442 44261 44258 44257 44441"
## [249] "PMC8335167 /pmc/articles/PMC8335167/bin/Data_Sheet_1.xlsx Hsapiens 24 44531 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44446 44447 44448"
## [250] "PMC8335167 /pmc/articles/PMC8335167/bin/Data_Sheet_1.xlsx Hsapiens 26 44440 44454 44264 44447 44531 44257 44441 44446 44256 44260 44263 44261 44450 44266 44443 44258 44259 44257 44442 44256 44451 44262 44265 44453 44449 44448"
## [251] "PMC8321682 /pmc/articles/PMC8321682/bin/LSA-2020-00996_TableS3.xls Dmelanogaster 3 37135 37500 38231"
## [252] "PMC8321653 /pmc/articles/PMC8321653/bin/LSA-2021-01019_TableS1.xlsx Hsapiens 1 37226"
## [253] "PMC8330917 /pmc/articles/PMC8330917/bin/pgen.1009681.s011.xlsx Hsapiens 23 40787 38961 39692 37316 37681 39142 39873 41883 39326 40057 38412 37316 37500 36951 38777 40422 37865 38231 39508 40238 40603 37226 38047"
## [254] "PMC8329287 /pmc/articles/PMC8329287/bin/41418_2021_769_MOESM9_ESM.xlsx Hsapiens 22 44256 44256 44449 44266 44266 44450 44450 44257 44257 44259 44259 44260 44261 44262 44262 44446 44446 44446 44264 44264 44448 44448"
## [255] "PMC8329071 /pmc/articles/PMC8329071/bin/41598_2021_95009_MOESM6_ESM.xlsx Hsapiens 4 38200 37104 37834 37469"
## [256] "PMC8322386 /pmc/articles/PMC8322386/bin/41467_2021_24919_MOESM3_ESM.xls Hsapiens 33 44166 43891 43892 43891 43891 43900 43901 43892 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44075 44084 44085 44086 44088 44076 44077 44078 44078 44079 44079 44080 44081 44082 44083"
## [257] "PMC8322386 /pmc/articles/PMC8322386/bin/41467_2021_24919_MOESM3_ESM.xls Hsapiens 33 44166 43891 43892 43891 43891 43900 43901 43892 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44075 44084 44085 44086 44088 44076 44077 44078 44078 44079 44079 44080 44081 44082 44083"
## [258] "PMC8316582 /pmc/articles/PMC8316582/bin/41467_2021_24824_MOESM5_ESM.xlsx Hsapiens 12 43897 43893 43901 43896 43899 43891 43900 43892 44166 43898 43895 43894"
## [259] "PMC8316576 /pmc/articles/PMC8316576/bin/41467_2021_24800_MOESM8_ESM.xlsx Mmusculus 7 9-Sep 9-Sep 9-Sep 9-Sep 8-Sep 3-Mar 3-Mar"
## [260] "PMC8316576 /pmc/articles/PMC8316576/bin/41467_2021_24800_MOESM9_ESM.xlsx Mmusculus 40 1-Mar 1-Mar 10-Mar 10-Mar 10-Mar 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 9-Sep 8-Sep 8-Sep 4-Sep 5-Sep 5-Sep 5-Sep 12-Sep 3-Mar 3-Mar 3-Mar 3-Mar 11-Sep 11-Sep 11-Sep 1-Sep"
## [261] "PMC8316550 /pmc/articles/PMC8316550/bin/41467_2021_24482_MOESM12_ESM.xlsx Hsapiens 2 44079 44079"
## [262] "PMC8316550 /pmc/articles/PMC8316550/bin/41467_2021_24482_MOESM12_ESM.xlsx Hsapiens 7 44079 44079 44079 44079 44079 44079 44079"
## [263] "PMC8316454 /pmc/articles/PMC8316454/bin/41467_2021_24781_MOESM5_ESM.xlsx Hsapiens 22 43891 43892 43891 43892 43893 43894 43895 43896 43897 43898 43899 44089 44084 44085 44076 44077 44078 44079 44080 44081 44082 44083"
## [264] "PMC8316454 /pmc/articles/PMC8316454/bin/41467_2021_24781_MOESM6_ESM.xlsx Hsapiens 1 43344"
## [265] "PMC8316454 /pmc/articles/PMC8316454/bin/41467_2021_24781_MOESM7_ESM.xlsx Hsapiens 1 43901"
## [266] "PMC8316454 /pmc/articles/PMC8316454/bin/41467_2021_24781_MOESM8_ESM.xlsx Hsapiens 1 44086"
## [267] "PMC8327752 /pmc/articles/PMC8327752/bin/Table_1.XLSX Hsapiens 12 43896 43897 43893 43892 43895 43899 44166 43891 43901 43894 43898 43900"
## [268] "PMC8327752 /pmc/articles/PMC8327752/bin/Table_1.XLSX Hsapiens 3 43896 43897 43893"
## [269] "PMC8327752 /pmc/articles/PMC8327752/bin/Table_1.XLSX Hsapiens 3 43897 43893 43896"
## [270] "PMC8327752 /pmc/articles/PMC8327752/bin/Table_1.XLSX Hsapiens 1 44262"
## [271] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43900 44075 43894 43899 44079 44080 43896 43901 44086 43898 44166 44077 43891 43892 44088 43893 44083 44078 44081 43897 44089 44084 43895 44076 44082 44085"
## [272] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 44079 44080 44075 43894 44078 43900 43901 43898 44077 43891 43892 44081 43899 44166 44086 44089 44088 43893 44085 44083 44082 43896 44076 43895 43897 44084"
## [273] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43899 43900 44166 44088 44083 43895 43896 43893 44086 43901 43897 44079 44077 44084 43892 43894 44089 44076 44075 44081 43898 44082 44078 44085 43891 44080"
## [274] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 44089 43897 44076 44081 43895 44085 44084 43891 44088 44166 43893 44075 43896 44080 44086 44078 43898 43892 44077 44082 44083 43901 43900 44079 43894 43899"
## [275] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43897 43898 44085 44084 44076 44081 43896 43891 43895 44082 44089 44080 44077 44166 43901 43893 43894 44088 44078 44086 44075 44079 43900 44083 43892 43899"
## [276] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43898 43896 43901 43893 43897 43891 44166 43894 44080 44086 44084 43895 44076 44075 44077 44081 44088 43900 44085 44078 43899 44089 44082 44079 44083 43892"
## [277] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43898 43891 44080 43896 43897 44082 44085 44084 44081 44076 44078 44075 43893 43894 44077 43901 44079 43895 44166 44086 44089 44088 43900 43899 43892 44083"
## [278] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 44089 44083 43895 43897 44081 44084 43896 44086 44076 43900 44166 43893 43891 44088 43899 44082 44085 44075 44080 43901 44077 43894 43898 44078 44079 43892"
## [279] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43898 43895 43896 44084 44076 44085 43897 43891 44081 43893 44082 44080 44166 43901 44088 44089 44086 44077 43894 44075 44083 44078 43900 44079 43892 43899"
## [280] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43897 44083 44089 44081 43895 44166 44076 44082 44085 44084 44088 43891 44075 44078 43892 43896 43900 43899 44080 44077 44086 44079 43893 43898 43901 43894"
## [281] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 44083 43895 44084 44088 43896 43897 44085 43899 44076 44082 44166 44089 43900 44086 44081 43893 43891 43892 43898 43901 44077 44080 44075 43894 44079 44078"
## [282] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43532 43530 43715 43525 43716 43528 43710 43719 43718 43535 43711 43714 43713 43531 43534 43527 43712 43723 43720 43800 43722 43709 43529 43533 43717 43526"
## [283] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43897 44084 43895 44076 44089 44085 44081 44082 44088 44083 44166 43896 43893 43891 43900 44086 43899 44077 44078 43898 44080 43892 43901 44075 43894 44079"
## [284] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43891 44080 44075 44078 44081 44089 44079 43901 44076 43898 43897 43894 44085 43892 44082 43895 44166 44077 43893 44083 43900 44086 43896 43899 44088 44084"
## [285] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43898 43896 44085 44084 44081 44076 43897 44089 43891 43895 44082 44077 44088 44080 44166 43901 43894 44086 44083 43893 43900 44075 44078 44079 43892 43899"
## [286] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 44075 43901 43891 43897 44080 43898 43894 43900 44086 43893 43896 44077 44078 44081 43895 44084 44076 44089 44166 44083 44079 43899 44085 44088 43892 44082"
## [287] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43897 43896 44089 43891 44084 44076 43893 43898 44075 44080 44085 43895 44086 44081 44083 44088 44166 44082 44077 44078 43892 43901 43900 43894 43899 44079"
## [288] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 44079 43901 43894 44083 43900 44088 43898 44089 44080 44077 44075 44081 44166 44086 43892 44085 44078 43891 44076 44084 44082 43899 43897 43896 43895 43893"
## [289] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43898 44085 43891 44076 44081 44084 43897 43896 44082 44080 43901 44077 44166 43894 43895 44078 44089 44088 43893 44075 44079 44086 43900 44083 43892 43899"
## [290] "PMC8325265 /pmc/articles/PMC8325265/bin/12967_2021_3001_MOESM10_ESM.xlsx Hsapiens 26 43898 44081 44085 44076 44082 43891 44077 44078 44080 43894 44079 44089 44084 43901 43896 43897 44166 44075 43900 44088 43895 43893 44086 43892 43899 44083"
## [291] "PMC8325178 /pmc/articles/PMC8325178/bin/13046_2021_2037_MOESM3_ESM.xlsx Hsapiens 2 42248 38961"
## [292] "PMC8324785 /pmc/articles/PMC8324785/bin/41398_2021_1480_MOESM2_ESM.xlsx Hsapiens 15 37135 37500 41883 37226 38231 41153 40057 40787 42248 40422 38108 39326 39692 37012 37865"
## [293] "PMC8323712 /pmc/articles/PMC8323712/bin/cir-144-353-s002.xlsx Hsapiens 13 44082 44078 44075 43897 44085 43898 43892 43892 44076 43895 44086 44081 44084"
## [294] "PMC8323712 /pmc/articles/PMC8323712/bin/cir-144-353-s002.xlsx Hsapiens 13 44085 44082 44084 44086 44081 44076 43898 44078 43897 43895 43892 43892 44075"In depth look at the errors
Let’s investigate the errors in more detail.
# By species
SPECIES <- sapply(strsplit(ERROR_GENELISTS," "),"[[",3)
table(SPECIES)## SPECIES
## Athaliana Dmelanogaster Drerio Ggallus Hsapiens
## 1 19 1 5 224
## Mmusculus Rnorvegicus
## 37 7par(mar=c(5,12,4,2))
barplot(table(SPECIES),horiz=TRUE,las=1)
par(mar=c(5,5,4,2))
# Number of affected Excel files per paper
DIST <- table(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
DIST##
## PMC8295287 PMC8298472 PMC8302675 PMC8316454 PMC8316550 PMC8316576 PMC8316582
## 4 1 5 4 2 2 1
## PMC8321653 PMC8321682 PMC8322386 PMC8323604 PMC8323712 PMC8324785 PMC8325178
## 1 1 2 1 2 1 1
## PMC8325244 PMC8325265 PMC8325267 PMC8326637 PMC8327752 PMC8329071 PMC8329287
## 1 20 2 1 4 1 1
## PMC8330917 PMC8333418 PMC8333778 PMC8335167 PMC8336464 PMC8339674 PMC8340308
## 1 1 1 4 1 14 1
## PMC8343164 PMC8344058 PMC8344067 PMC8345867 PMC8346036 PMC8346558 PMC8346570
## 22 1 3 3 2 4 1
## PMC8346669 PMC8350206 PMC8350412 PMC8350897 PMC8351575 PMC8351597 PMC8352595
## 1 2 1 3 1 3 9
## PMC8352870 PMC8352983 PMC8353259 PMC8353793 PMC8354477 PMC8355218 PMC8355708
## 1 3 1 2 2 1 6
## PMC8355820 PMC8355892 PMC8356190 PMC8357189 PMC8357785 PMC8357835 PMC8357957
## 3 1 1 1 1 2 1
## PMC8358448 PMC8359384 PMC8361032 PMC8361094 PMC8361107 PMC8361881 PMC8362890
## 4 1 1 10 4 1 1
## PMC8362953 PMC8363264 PMC8363306 PMC8363664 PMC8365341 PMC8366456 PMC8367384
## 1 1 1 2 1 1 13
## PMC8369001 PMC8369824 PMC8370613 PMC8371109 PMC8372368 PMC8378686 PMC8379442
## 2 1 2 1 8 3 1
## PMC8379831 PMC8381363 PMC8383299 PMC8384091 PMC8384175 PMC8386026 PMC8386078
## 1 1 2 1 47 1 2
## PMC8386171 PMC8386547 PMC8386872 PMC8387103 PMC8389471
## 2 1 2 7 4summary(as.numeric(DIST))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.000 1.000 1.000 3.303 3.000 47.000hist(DIST,main="Number of affected Excel files per paper")
# PMC Articles with the most errors
DIST_DF <- as.data.frame(DIST)
DIST_DF <- DIST_DF[order(-DIST_DF$Freq),,drop=FALSE]
head(DIST_DF,20)## Var1 Freq
## 82 PMC8384175 47
## 29 PMC8343164 22
## 16 PMC8325265 20
## 27 PMC8339674 14
## 70 PMC8367384 13
## 60 PMC8361094 10
## 42 PMC8352595 9
## 75 PMC8372368 8
## 88 PMC8387103 7
## 49 PMC8355708 6
## 3 PMC8302675 5
## 1 PMC8295287 4
## 4 PMC8316454 4
## 19 PMC8327752 4
## 25 PMC8335167 4
## 34 PMC8346558 4
## 57 PMC8358448 4
## 61 PMC8361107 4
## 89 PMC8389471 4
## 31 PMC8344067 3MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES## [1] "PMC8384175"# Number of errors per paper
NERR <- as.numeric(sapply(strsplit(ERROR_GENELISTS," "),"[[",4))
names(NERR) <- sapply(strsplit(ERROR_GENELISTS," "),"[[",1)
NERR <-tapply(NERR, names(NERR), sum)
NERR## PMC8295287 PMC8298472 PMC8302675 PMC8316454 PMC8316550 PMC8316576 PMC8316582
## 34 3 7 25 9 47 12
## PMC8321653 PMC8321682 PMC8322386 PMC8323604 PMC8323712 PMC8324785 PMC8325178
## 1 3 66 1 26 15 2
## PMC8325244 PMC8325265 PMC8325267 PMC8326637 PMC8327752 PMC8329071 PMC8329287
## 14 520 5 10 19 4 22
## PMC8330917 PMC8333418 PMC8333778 PMC8335167 PMC8336464 PMC8339674 PMC8340308
## 23 1 28 100 4 483 5
## PMC8343164 PMC8344058 PMC8344067 PMC8345867 PMC8346036 PMC8346558 PMC8346570
## 139 11 12 9 68 57 3
## PMC8346669 PMC8350206 PMC8350412 PMC8350897 PMC8351575 PMC8351597 PMC8352595
## 5 68 1 5 7 35 96
## PMC8352870 PMC8352983 PMC8353259 PMC8353793 PMC8354477 PMC8355218 PMC8355708
## 4 74 5 2 33 49 6
## PMC8355820 PMC8355892 PMC8356190 PMC8357189 PMC8357785 PMC8357835 PMC8357957
## 12 1 1 8 25 13 3
## PMC8358448 PMC8359384 PMC8361032 PMC8361094 PMC8361107 PMC8361881 PMC8362890
## 8 1 28 175 29 7 5
## PMC8362953 PMC8363264 PMC8363306 PMC8363664 PMC8365341 PMC8366456 PMC8367384
## 21 80 1 2 7 10 30
## PMC8369001 PMC8369824 PMC8370613 PMC8371109 PMC8372368 PMC8378686 PMC8379442
## 28 2 2 1 119 7 1
## PMC8379831 PMC8381363 PMC8383299 PMC8384091 PMC8384175 PMC8386026 PMC8386078
## 167 25 8 28 684 21 18
## PMC8386171 PMC8386547 PMC8386872 PMC8387103 PMC8389471
## 6 1 62 104 202hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
head(NERR_DF,20)## NERR
## PMC8384175 684
## PMC8325265 520
## PMC8339674 483
## PMC8389471 202
## PMC8361094 175
## PMC8379831 167
## PMC8343164 139
## PMC8372368 119
## PMC8387103 104
## PMC8335167 100
## PMC8352595 96
## PMC8363264 80
## PMC8352983 74
## PMC8346036 68
## PMC8350206 68
## PMC8322386 66
## PMC8386872 62
## PMC8346558 57
## PMC8355218 49
## PMC8316576 47MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR## [1] "PMC8384175"Journals affected
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
### JSON PARSING is more reliable than XML
ARTICLES <- esummary( GENELIST_ERROR_ARTICLES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA$result
ARTICLE_DATA <- ARTICLE_DATA[2:length(ARTICLE_DATA)]
JOURNALS <- unlist(lapply(ARTICLE_DATA,function(x) {x$fulljournalname} ))
JOURNALS_TABLE <- table(JOURNALS)
JOURNALS_TABLE <- JOURNALS_TABLE[order(-JOURNALS_TABLE)]
length(JOURNALS_TABLE)## [1] 47NUM_JOURNALS=length(JOURNALS_TABLE)
par(mar=c(5,25,4,2))
barplot(head(JOURNALS_TABLE,10), horiz=TRUE, las=1,
xlab="Articles with gene name errors in supp files",
main="Top journals this month")
Journal of the month winner
Congrats to our Journal of the Month winner!
JOURNAL_WINNER <- names(head(JOURNALS_TABLE,1))
JOURNAL_WINNER## [1] "Nature Communications"Paper of the month winners
There are two categories:
Paper with the most suplementary files affected by gene name errors (MOST_ERR_FILES)
Paper with the most gene names converted to dates (MOST_ERR)
Sometimes, one paper can win both categories. Congrats to our winners.
Paper with most files affected
MOST_ERR_FILES <- gsub("PMC","",MOST_ERR_FILES)
ARTICLES <- esummary( MOST_ERR_FILES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA[2]
ARTICLE_DATA## $result
## $result$uids
## [1] "8384175"
##
## $result$`8384175`
## $result$`8384175`$uid
## [1] "8384175"
##
## $result$`8384175`$pubdate
## [1] "2021 Aug 12"
##
## $result$`8384175`$epubdate
## [1] "2021 Aug 12"
##
## $result$`8384175`$printpubdate
## [1] ""
##
## $result$`8384175`$source
## [1] "PLoS Comput Biol"
##
## $result$`8384175`$authors
## name authtype
## 1 Duan R Author
## 2 Gao L Author
## 3 Gao Y Author
## 4 Hu Y Author
## 5 Xu H Author
## 6 Huang M Author
## 7 Song K Author
## 8 Wang H Author
## 9 Dong Y Author
## 10 Jiang C Author
## 11 Zhang C Author
## 12 Jia S Author
##
## $result$`8384175`$title
## [1] "Evaluation and comparison of multi-omics data integration methods for cancer subtyping"
##
## $result$`8384175`$volume
## [1] "17"
##
## $result$`8384175`$issue
## [1] "8"
##
## $result$`8384175`$pages
## [1] "e1009224"
##
## $result$`8384175`$articleids
## idtype value
## 1 pmid 34383739
## 2 doi 10.1371/journal.pcbi.1009224
## 3 pmcid PMC8384175
##
## $result$`8384175`$fulljournalname
## [1] "PLoS Computational Biology"
##
## $result$`8384175`$sortdate
## [1] "2021/08/12 00:00"
##
## $result$`8384175`$pmclivedate
## [1] "2021/08/25"Paper with most date conversions
MOST_ERR <- gsub("PMC","",MOST_ERR)
ARTICLE_DATA <- esummary(MOST_ERR,db = "pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLE_DATA,as= "parsed")
ARTICLE_DATA## $header
## $header$type
## [1] "esummary"
##
## $header$version
## [1] "0.3"
##
##
## $result
## $result$uids
## [1] "8384175"
##
## $result$`8384175`
## $result$`8384175`$uid
## [1] "8384175"
##
## $result$`8384175`$pubdate
## [1] "2021 Aug 12"
##
## $result$`8384175`$epubdate
## [1] "2021 Aug 12"
##
## $result$`8384175`$printpubdate
## [1] ""
##
## $result$`8384175`$source
## [1] "PLoS Comput Biol"
##
## $result$`8384175`$authors
## name authtype
## 1 Duan R Author
## 2 Gao L Author
## 3 Gao Y Author
## 4 Hu Y Author
## 5 Xu H Author
## 6 Huang M Author
## 7 Song K Author
## 8 Wang H Author
## 9 Dong Y Author
## 10 Jiang C Author
## 11 Zhang C Author
## 12 Jia S Author
##
## $result$`8384175`$title
## [1] "Evaluation and comparison of multi-omics data integration methods for cancer subtyping"
##
## $result$`8384175`$volume
## [1] "17"
##
## $result$`8384175`$issue
## [1] "8"
##
## $result$`8384175`$pages
## [1] "e1009224"
##
## $result$`8384175`$articleids
## idtype value
## 1 pmid 34383739
## 2 doi 10.1371/journal.pcbi.1009224
## 3 pmcid PMC8384175
##
## $result$`8384175`$fulljournalname
## [1] "PLoS Computational Biology"
##
## $result$`8384175`$sortdate
## [1] "2021/08/12 00:00"
##
## $result$`8384175`$pmclivedate
## [1] "2021/08/25"Trend info
To plot the trend over the past 6-12 months.
url <- "http://ziemann-lab.net/public/gene_name_errors/"
doc <- htmlParse(url)
links <- xpathSApply(doc, "//a/@href")
links <- links[grep("html",links)]
links## href href href
## "Report_2021-02.html" "Report_2021-03.html" "Report_2021-04.html"
## href href href
## "Report_2021-05.html" "Report_2021-06.html" "Report_2021-07.html"
## href
## "Report_2021-08.html"unlink("online_files/",recursive=TRUE)
dir.create("online_files")
sapply(links, function(mylink) {
download.file(paste(url,mylink,sep=""),destfile=paste("online_files/",mylink,sep=""))
} )## href href href href href href href
## 0 0 0 0 0 0 0myfilelist <- list.files("online_files/",full.names=TRUE)
trends <- sapply(myfilelist, function(myfilename) {
x <- readLines(myfilename)
# Num XL gene list articles
NUM_GENELIST_ARTICLES <- x[grep("NUM_GENELIST_ARTICLES",x)[3]+1]
NUM_GENELIST_ARTICLES <- sapply(strsplit(NUM_GENELIST_ARTICLES," "),"[[",3)
NUM_GENELIST_ARTICLES <- sapply(strsplit(NUM_GENELIST_ARTICLES,"<"),"[[",1)
NUM_GENELIST_ARTICLES <- as.numeric(NUM_GENELIST_ARTICLES)
# number of affected articles
NUM_ERROR_GENELIST_ARTICLES <- x[grep("NUM_ERROR_GENELIST_ARTICLES",x)[3]+1]
NUM_ERROR_GENELIST_ARTICLES <- sapply(strsplit(NUM_ERROR_GENELIST_ARTICLES," "),"[[",3)
NUM_ERROR_GENELIST_ARTICLES <- sapply(strsplit(NUM_ERROR_GENELIST_ARTICLES,"<"),"[[",1)
NUM_ERROR_GENELIST_ARTICLES <- as.numeric(NUM_ERROR_GENELIST_ARTICLES)
# Error proportion
ERROR_PROPORTION <- x[grep("ERROR_PROPORTION",x)[3]+1]
ERROR_PROPORTION <- sapply(strsplit(ERROR_PROPORTION," "),"[[",3)
ERROR_PROPORTION <- sapply(strsplit(ERROR_PROPORTION,"<"),"[[",1)
ERROR_PROPORTION <- as.numeric(ERROR_PROPORTION)
# number of journals
NUM_JOURNALS <- x[grep('JOURNALS_TABLE',x)[3]+1]
NUM_JOURNALS <- sapply(strsplit(NUM_JOURNALS," "),"[[",3)
NUM_JOURNALS <- sapply(strsplit(NUM_JOURNALS,"<"),"[[",1)
NUM_JOURNALS <- as.numeric(NUM_JOURNALS)
NUM_JOURNALS
res <- c(NUM_GENELIST_ARTICLES,NUM_ERROR_GENELIST_ARTICLES,ERROR_PROPORTION,NUM_JOURNALS)
return(res)
})
colnames(trends) <- sapply(strsplit(colnames(trends),"_"),"[[",3)
colnames(trends) <- gsub(".html","",colnames(trends))
trends <- as.data.frame(trends)
rownames(trends) <- c("NUM_GENELIST_ARTICLES","NUM_ERROR_GENELIST_ARTICLES","ERROR_PROPORTION","NUM_JOURNALS")
trends <- t(trends)
trends <- as.data.frame(trends)
CURRENT_RES <- c(NUM_GENELIST_ARTICLES,NUM_ERROR_GENELIST_ARTICLES,ERROR_PROPORTION,NUM_JOURNALS)
trends <- rbind(trends,CURRENT_RES)
paste(CURRENT_YEAR,CURRENT_MONTH,sep="-")## [1] "2021-09"rownames(trends)[nrow(trends)] <- paste(CURRENT_YEAR,CURRENT_MONTH,sep="-")
plot(trends$NUM_GENELIST_ARTICLES, xaxt = "n" , type="b" , main="Number of articles with Excel gene lists per month",
ylab="number of articles", xlab="month")
axis(1, at=1:nrow(trends), labels=rownames(trends))
plot(trends$NUM_ERROR_GENELIST_ARTICLES, xaxt = "n" , type="b" , main="Number of articles with gene name errors per month",
ylab="number of articles", xlab="month")
axis(1, at=1:nrow(trends), labels=rownames(trends))
plot(trends$ERROR_PROPORTION, xaxt = "n" , type="b" , main="Proportion of articles with Excel gene list affected by errors",
ylab="proportion", xlab="month")
axis(1, at=1:nrow(trends), labels=rownames(trends))
plot(trends$NUM_JOURNALS, xaxt = "n" , type="b" , main="Number of journals with affected articles",
ylab="number of journals", xlab="month")
axis(1, at=1:nrow(trends), labels=rownames(trends))
unlink("online_files/",recursive=TRUE)References
Zeeberg, B.R., Riss, J., Kane, D.W. et al. Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics 5, 80 (2004). https://doi.org/10.1186/1471-2105-5-80
Ziemann, M., Eren, Y. & El-Osta, A. Gene name errors are widespread in the scientific literature. Genome Biol 17, 177 (2016). https://doi.org/10.1186/s13059-016-1044-7
SessionInfo
sessionInfo()## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] readxl_1.3.1 reutils_0.2.3 xml2_1.3.2 jsonlite_1.7.2 XML_3.99-0.6
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 knitr_1.33 magrittr_2.0.1 R6_2.5.1
## [5] rlang_0.4.11 fastmap_1.1.0 highr_0.9 stringr_1.4.0
## [9] tools_4.1.0 xfun_0.25 jquerylib_0.1.4 htmltools_0.5.2
## [13] yaml_2.2.1 digest_0.6.27 assertthat_0.2.1 sass_0.4.0
## [17] bitops_1.0-7 RCurl_1.98-1.3 evaluate_0.14 rmarkdown_2.10
## [21] stringi_1.7.4 compiler_4.1.0 bslib_0.2.5.1 cellranger_1.1.0