Gene Name Error Monthly Dashboard
Mark Ziemann
2021-06-08
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("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.
DATE="2021/3"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 3500## Retrieving UIDs 3501 to 4000pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 3539writeLines(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] 4562NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 751GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 604NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 295ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 323GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC7994849" "PMC7981925" "PMC7981997" "PMC7973504" "PMC7968368"
## [6] "PMC7968334" "PMC7984841" "PMC7958471" "PMC7958140" "PMC7955039"
## [11] "PMC7990797" "PMC7987945" "PMC7946903" "PMC7946432" "PMC7982637"
## [16] "PMC7942016" "PMC7942004" "PMC7982650" "PMC7980453" "PMC7980388"
## [21] "PMC7941712" "PMC7940623" "PMC7939296" "PMC7999279" "PMC7973040"
## [26] "PMC7935873" "PMC7939520" "PMC7934504" "PMC7934467" "PMC7933180"
## [31] "PMC7932549" "PMC7958240" "PMC7931766" "PMC7928942" "PMC7925591"
## [36] "PMC7956951" "PMC7951976" "PMC7921423" "PMC7917095" "PMC7913449"
## [41] "PMC7913431" "PMC7953160" "PMC7910483" "PMC7910482" "PMC7910459"
## [46] "PMC7959850" "PMC7940259" "PMC7945945" "PMC7945594" "PMC7944992"
## [51] "PMC7943886" "PMC7903607" "PMC7935315" "PMC7902657" "PMC7937961"
## [56] "PMC7900196" "PMC7974522" "PMC7933519" "PMC7895368" "PMC7931689"
## [61] "PMC7930499" "PMC7924761" "PMC7905234" "PMC7892573" "PMC7892572"
## [66] "PMC7925823" "PMC7886901" "PMC7937391" "PMC7957197" "PMC7986194"
## [71] "PMC7910251" "PMC7906164" "PMC7892346" "PMC7892341" "PMC7906150"
## [76] "PMC7948421" "PMC7610462"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 77ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.2610169Look 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] "PMC7994849 /pmc/articles/PMC7994849/bin/41598_2021_86263_MOESM2_ESM.xlsx Hsapiens 1 44078"
## [2] "PMC7981925 /pmc/articles/PMC7981925/bin/12859_2021_4072_MOESM1_ESM.xlsx Hsapiens 13 42621 42437 42615 42705 42439 42432 42614 42628 42440 42622 42618 42623 42434"
## [3] "PMC7981997 /pmc/articles/PMC7981997/bin/12906_2021_3273_MOESM1_ESM.xlsx Ggallus 14 44076 43891 43893 43898 44085 44086 44082 44076 43894 43896 44075 44083 44089 44077"
## [4] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM2_ESM.xlsx Hsapiens 2 43717 43716"
## [5] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM2_ESM.xlsx Hsapiens 2 43717 43716"
## [6] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM2_ESM.xlsx Hsapiens 2 43717 43716"
## [7] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM2_ESM.xlsx Hsapiens 8 43714 43716 43717 43710 43529 43718 43715 43719"
## [8] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM2_ESM.xlsx Hsapiens 8 43714 43716 43717 43710 43529 43718 43715 43719"
## [9] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM2_ESM.xlsx Hsapiens 8 43714 43716 43717 43710 43529 43718 43715 43719"
## [10] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 1 43710"
## [11] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 1 43710"
## [12] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 1 43710"
## [13] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 6 43717 43716 43710 43719 43715 43718"
## [14] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 6 43717 43716 43710 43719 43715 43718"
## [15] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 6 43717 43716 43710 43719 43715 43718"
## [16] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 9 43529 43723 43710 43717 43716 43715 43719 43714 43718"
## [17] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 9 43529 43723 43710 43717 43716 43715 43719 43714 43718"
## [18] "PMC7973504 /pmc/articles/PMC7973504/bin/41598_2021_85342_MOESM3_ESM.xlsx Hsapiens 9 43529 43723 43710 43717 43716 43715 43719 43714 43718"
## [19] "PMC7968368 /pmc/articles/PMC7968368/bin/12931_2021_1679_MOESM2_ESM.xlsx Mmusculus 7 40238 40238 40603 40603 40603 40603 36951"
## [20] "PMC7968368 /pmc/articles/PMC7968368/bin/12931_2021_1679_MOESM2_ESM.xlsx Mmusculus 7 40238 40238 40603 40603 40603 40603 36951"
## [21] "PMC7968334 /pmc/articles/PMC7968334/bin/13073_2021_855_MOESM2_ESM.xlsx Hsapiens 1 44083"
## [22] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp1.xlsx Dmelanogaster 3 44079 44075 44079"
## [23] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp1.xlsx Dmelanogaster 5 44079 44075 44079 44075 44079"
## [24] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp1.xlsx Dmelanogaster 1 44079"
## [25] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp2.xlsx Dmelanogaster 5 44075 44076 44079 44078 44166"
## [26] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp2.xlsx Dmelanogaster 5 44075 44078 44079 44076 44166"
## [27] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp2.xlsx Dmelanogaster 5 44078 44075 44079 44076 44166"
## [28] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp5.xlsx Dmelanogaster 5 44076 44078 44079 44075 44166"
## [29] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp5.xlsx Dmelanogaster 5 44078 44075 44079 44076 44166"
## [30] "PMC7984841 /pmc/articles/PMC7984841/bin/elife-62250-supp5.xlsx Dmelanogaster 2 44078 44075"
## [31] "PMC7958471 /pmc/articles/PMC7958471/bin/13046_2021_1835_MOESM16_ESM.xlsx Hsapiens 3 43710 43715 43717"
## [32] "PMC7958471 /pmc/articles/PMC7958471/bin/13046_2021_1835_MOESM2_ESM.xlsx Hsapiens 3 43717 43710 43715"
## [33] "PMC7958140 /pmc/articles/PMC7958140/bin/13073_2021_859_MOESM15_ESM.xlsx Hsapiens 27 39508 41883 37316 36951 39692 38961 40787 41153 39508 40422 37316 38412 37681 39326 37500 38047 39873 37865 37135 36951 42248 37226 38231 38596 40057 38777 39142"
## [34] "PMC7958140 /pmc/articles/PMC7958140/bin/13073_2021_859_MOESM16_ESM.xlsx Hsapiens 26 40057 38596 39873 37316 40787 40057 41883 37226 38961 40422 38777 39508 37500 38047 38231 37865 39326 42248 37316 37135 39142 38412 37681 39692 39508 36951"
## [35] "PMC7955039 /pmc/articles/PMC7955039/bin/41467_2021_21854_MOESM4_ESM.xlsx Hsapiens 1 43532"
## [36] "PMC7955039 /pmc/articles/PMC7955039/bin/41467_2021_21854_MOESM4_ESM.xlsx Hsapiens 1 43532"
## [37] "PMC7990797 /pmc/articles/PMC7990797/bin/Table_1.XLSX Hsapiens 27 42795 42794 42984 42795 42985 42986 42804 42802 42798 42982 42796 42797 42987 42799 42801 42991 43069 42978 42981 42989 42988 42980 42794 42800 42979 42803 42983"
## [38] "PMC7990797 /pmc/articles/PMC7990797/bin/Table_3.XLSX Hsapiens 3 44260 44445 44257"
## [39] "PMC7987945 /pmc/articles/PMC7987945/bin/Table_2.XLSX Hsapiens 9 8-Mar 2-Mar 6-Mar 1-Mar 3-Mar 5-Mar 11-Mar 7-Mar 4-Mar"
## [40] "PMC7987945 /pmc/articles/PMC7987945/bin/Table_3.XLSX Hsapiens 9 1-Mar 2-Mar 3-Mar 4-Mar 5-Mar 6-Mar 7-Mar 8-Mar 11-Mar"
## [41] "PMC7987945 /pmc/articles/PMC7987945/bin/Table_4.XLSX Ggallus 8 2-Mar 8-Mar 1-Mar 7-Mar 5-Mar 6-Mar 3-Mar 11-Mar"
## [42] "PMC7946903 /pmc/articles/PMC7946903/bin/41467_2021_21661_MOESM4_ESM.xlsx Hsapiens 10 39692 37500 38961 40787 37865 40057 37135 38596 40422 39326"
## [43] "PMC7946903 /pmc/articles/PMC7946903/bin/41467_2021_21661_MOESM4_ESM.xlsx Hsapiens 10 37135 40787 40422 37865 38961 40057 38231 39692 39326 37500"
## [44] "PMC7946903 /pmc/articles/PMC7946903/bin/41467_2021_21661_MOESM4_ESM.xlsx Hsapiens 10 37135 40422 40787 37500 39692 38961 38596 39326 40057 37865"
## [45] "PMC7946903 /pmc/articles/PMC7946903/bin/41467_2021_21661_MOESM4_ESM.xlsx Hsapiens 10 39692 40422 38961 40057 37865 37500 38596 40787 37135 39326"
## [46] "PMC7946903 /pmc/articles/PMC7946903/bin/41467_2021_21661_MOESM4_ESM.xlsx Hsapiens 10 39692 38231 40057 40787 37865 37135 37500 40422 38961 39326"
## [47] "PMC7946432 /pmc/articles/PMC7946432/bin/elife-60326-fig3-data1.xlsx Dmelanogaster 4 1-Sep 2-Sep 4-Sep 5-Sep"
## [48] "PMC7946432 /pmc/articles/PMC7946432/bin/elife-60326-fig3-data1.xlsx Dmelanogaster 1 5-Sep"
## [49] "PMC7946432 /pmc/articles/PMC7946432/bin/elife-60326-fig3-data1.xlsx Dmelanogaster 2 1-Sep 2-Sep"
## [50] "PMC7946432 /pmc/articles/PMC7946432/bin/elife-60326-fig4-data1.xlsx Dmelanogaster 1 44075"
## [51] "PMC7946432 /pmc/articles/PMC7946432/bin/elife-60326-supp2.xlsx Dmelanogaster 9 37500 37500 37500 37500 38231 38231 37135 37135 37135"
## [52] "PMC7982637 /pmc/articles/PMC7982637/bin/CAM4-10-2461-s001.xlsx Hsapiens 1 44448"
## [53] "PMC7942016 /pmc/articles/PMC7942016/bin/13059_2021_2287_MOESM10_ESM.xlsx Hsapiens 12 43714 43715 43531 43710 43715 43714 43717 43710 43710 43710 43710 43710"
## [54] "PMC7942016 /pmc/articles/PMC7942016/bin/13059_2021_2287_MOESM4_ESM.xlsx Hsapiens 1 43717"
## [55] "PMC7942004 /pmc/articles/PMC7942004/bin/12885_2021_7888_MOESM1_ESM.xlsx Hsapiens 17 43896 43899 44081 44089 44076 43895 44083 43891 43898 43892 43897 44082 44084 44085 43892 43893 44079"
## [56] "PMC7942004 /pmc/articles/PMC7942004/bin/12885_2021_7888_MOESM1_ESM.xlsx Hsapiens 17 43896 43899 44081 44089 44076 43895 44083 43891 43898 43892 43897 44082 44084 44085 43892 43893 44079"
## [57] "PMC7942004 /pmc/articles/PMC7942004/bin/12885_2021_7888_MOESM2_ESM.xlsx Hsapiens 27 43891 44079 44081 43901 44078 43901 43901 44078 43901 43896 44083 43901 43901 43894 44078 43892 44083 43892 43892 43892 43892 43900 43892 43891 44083 43892 44075"
## [58] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44257 44256 44261"
## [59] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44256 44257 44441"
## [60] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44440 44448"
## [61] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 7 44446 44443 44450 44441 44447 44449 44444"
## [62] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 5 44440 44446 44258 44448 44262"
## [63] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 1 44256"
## [64] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 1 44440"
## [65] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44440 44446 44448 44260"
## [66] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44256 44441"
## [67] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44440 44446 44258 44448"
## [68] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 6 44441 44449 44258 44446 44447 44257"
## [69] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 8 44256 44440 44448 44446 44262 44258 44264 44260"
## [70] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44257 44454 44256 44261"
## [71] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44441 44258 44446"
## [72] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44256 44454"
## [73] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 5 44443 44446 44450 44260 44441"
## [74] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44257 44256 44261"
## [75] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44261 44440 44262 44448"
## [76] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 1 44256"
## [77] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 6 44440 44261 44257 44446 44260 44448"
## [78] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 7 44450 44443 44446 44447 44441 44258 44449"
## [79] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44440 44263"
## [80] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 5 44256 44448 44257 44261 44454"
## [81] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 5 44441 44446 44258 44450 44264"
## [82] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44257 44256 44261"
## [83] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44256 44441"
## [84] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 7 44441 44258 44449 44446 44447 44259 44264"
## [85] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 6 44440 44261 44446 44260 44441 44454"
## [86] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 8 44443 44446 44450 44441 44444 44447 44449 44261"
## [87] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44440 44261 44454 44441"
## [88] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44256 44257 44448"
## [89] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44440 44446 44448"
## [90] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44256 44448"
## [91] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44440 44442"
## [92] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 8 44450 44446 44443 44447 44441 44449 44258 44444"
## [93] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44256 44440 44448 44446"
## [94] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 5 44440 44446 44261 44258 44260"
## [95] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 7 44446 44447 44256 44443 44263 44449 44261"
## [96] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44258 44262"
## [97] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 6 44258 44257 44448 44256 44261 44450"
## [98] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 6 44266 44259 44442 44450 44257 44256"
## [99] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44256 44264 44441"
## [100] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 5 44258 44262 44448 44450 44260"
## [101] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44450 44448 44262"
## [102] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44265 44257 44258 44256"
## [103] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 6 44259 44266 44450 44257 44442 44256"
## [104] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44450 44263 44448 44442"
## [105] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 9 44449 44441 44256 44447 44258 44443 44450 44257 44257"
## [106] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44440 44448 44261 44454"
## [107] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44256 44257"
## [108] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 6 44440 44446 44448 44260 44262 44450"
## [109] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 1 44257"
## [110] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44446 44440 44260"
## [111] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 9 44256 44264 44258 44440 44261 44263 44454 44446 44448"
## [112] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44256 44257"
## [113] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 7 44446 44440 44261 44448 44260 44450 44262"
## [114] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 3 44256 44257 44260"
## [115] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 7 44443 44450 44446 44444 44447 44449 44257"
## [116] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 2 44256 44257"
## [117] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 1 44442"
## [118] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 4 44440 44448 44257 44446"
## [119] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 6 44449 44258 44441 44257 44450 44444"
## [120] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 8 44264 44256 44454 44257 44448 44440 44450 44441"
## [121] "PMC7982650 /pmc/articles/PMC7982650/bin/Data_Sheet_2.xlsx Hsapiens 5 44441 44450 44256 44257 44449"
## [122] "PMC7980453 /pmc/articles/PMC7980453/bin/pnas.2016274118.sd03.xlsx Hsapiens 42 44084 44086 43893 33556 28631 44080 43891 43900 43894 37494 43896 44088 43898 43892 44085 43892 44082 44079 43894 31430 44076 44080 43892 43897 33556 44075 43894 43895 43891 44081 44078 43899 43900 28712 35315 44083 44088 33533 44088 43901 44083 44076"
## [123] "PMC7980453 /pmc/articles/PMC7980453/bin/pnas.2016274118.sd03.xlsx Hsapiens 35 44084 44086 43893 33556 28631 44080 43891 43900 43894 43896 44088 43898 43892 44085 44082 44079 43894 44076 44080 43892 43897 33556 44075 43894 43895 43891 44078 43899 43900 44083 44088 44088 43901 44083 44076"
## [124] "PMC7980388 /pmc/articles/PMC7980388/bin/pnas.2020152118.sd03.xlsx Mmusculus 2 40422 37316"
## [125] "PMC7941712 /pmc/articles/PMC7941712/bin/40478_2021_1135_MOESM10_ESM.xlsx Mmusculus 2 44085 44082"
## [126] "PMC7941712 /pmc/articles/PMC7941712/bin/40478_2021_1135_MOESM10_ESM.xlsx Mmusculus 1 44085"
## [127] "PMC7941712 /pmc/articles/PMC7941712/bin/40478_2021_1135_MOESM12_ESM.xlsx Hsapiens 4 44448 44448 44445 44448"
## [128] "PMC7941712 /pmc/articles/PMC7941712/bin/40478_2021_1135_MOESM12_ESM.xlsx Hsapiens 10 44257 44258 44257 44258 44450 44450 44257 44265 44442 44256"
## [129] "PMC7941712 /pmc/articles/PMC7941712/bin/40478_2021_1135_MOESM9_ESM.xlsx Hsapiens 1 43531"
## [130] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [131] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [132] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [133] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [134] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [135] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [136] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [137] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [138] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [139] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [140] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [141] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [142] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM10_ESM.xlsx Hsapiens 1 43892"
## [143] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM14_ESM.xlsx Hsapiens 1 44256"
## [144] "PMC7940623 /pmc/articles/PMC7940623/bin/41467_2021_21725_MOESM6_ESM.xlsx Hsapiens 6 43892 43891 43892 43891 43891 43891"
## [145] "PMC7939296 /pmc/articles/PMC7939296/bin/pone.0246650.s002.xlsx Hsapiens 3 40057 38961 37135"
## [146] "PMC7999279 zip/2.SupplementaryMaterial/TableS1.xlsx Ggallus 2 44081 44081"
## [147] "PMC7973040 /pmc/articles/PMC7973040/bin/Table_2.XLSX Mmusculus 2 43899 43897"
## [148] "PMC7973040 /pmc/articles/PMC7973040/bin/Table_2.XLSX Mmusculus 2 43897 44089"
## [149] "PMC7935873 /pmc/articles/PMC7935873/bin/41467_2021_21537_MOESM8_ESM.xlsx Dmelanogaster 4 44078 44076 44079 44075"
## [150] "PMC7935873 /pmc/articles/PMC7935873/bin/41467_2021_21537_MOESM8_ESM.xlsx Dmelanogaster 4 44076 44075 44078 44079"
## [151] "PMC7935873 /pmc/articles/PMC7935873/bin/41467_2021_21537_MOESM8_ESM.xlsx Dmelanogaster 4 44075 44076 44078 44079"
## [152] "PMC7935873 /pmc/articles/PMC7935873/bin/41467_2021_21537_MOESM8_ESM.xlsx Dmelanogaster 4 44078 44075 44079 44076"
## [153] "PMC7939520 /pmc/articles/PMC7939520/bin/mmc2.xlsx Hsapiens 18 38047 40787 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 40603 41883 39508 40238 40238 40057"
## [154] "PMC7939520 /pmc/articles/PMC7939520/bin/mmc2.xlsx Ggallus 2 36951 40057"
## [155] "PMC7939520 /pmc/articles/PMC7939520/bin/mmc2.xlsx Hsapiens 31 39142 38047 37500 37500 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 38777 40603 40603 40603 37681 37681 39326 39326 39326 37226 38412 40057 40057 40057"
## [156] "PMC7939520 /pmc/articles/PMC7939520/bin/mmc2.xlsx Hsapiens 1 36951"
## [157] "PMC7934504 /pmc/articles/PMC7934504/bin/12860_2021_352_MOESM12_ESM.xlsx Hsapiens 3 40057 39326 37500"
## [158] "PMC7934504 /pmc/articles/PMC7934504/bin/12860_2021_352_MOESM8_ESM.xlsx Hsapiens 3 44083 44081 44076"
## [159] "PMC7934504 /pmc/articles/PMC7934504/bin/12860_2021_352_MOESM9_ESM.xlsx Hsapiens 1 37500"
## [160] "PMC7934467 /pmc/articles/PMC7934467/bin/12859_2021_4046_MOESM5_ESM.xlsx Hsapiens 19 43525 43525 43534 43526 43527 43528 43529 43530 43531 43532 43533 43718 43710 43711 43713 43714 43715 43716 43717"
## [161] "PMC7933180 /pmc/articles/PMC7933180/bin/41398_2021_1270_MOESM1_ESM.xlsx Hsapiens 18 43893 43898 44075 44078 43891 44080 44082 44085 43892 43891 44081 44083 44076 43897 43895 43899 43896 44084"
## [162] "PMC7932549 /pmc/articles/PMC7932549/bin/pone.0247837.s002.xlsx Hsapiens 1 43891"
## [163] "PMC7958240 /pmc/articles/PMC7958240/bin/pnas.2022172118.sd01.xlsx Mmusculus 26 39692 38596 39326 37865 40787 38231 38777 38961 36951 38412 39508 37316 40422 40057 39142 37316 40238 38047 39873 37135 40603 41153 37500 36951 37681 41883"
## [164] "PMC7958240 /pmc/articles/PMC7958240/bin/pnas.2022172118.sd01.xlsx Mmusculus 26 38596 39692 37865 39326 38231 38777 40787 37316 38412 39142 38047 36951 38961 37316 40057 39508 40422 37135 37681 40238 39873 40603 41153 37500 36951 41883"
## [165] "PMC7958240 /pmc/articles/PMC7958240/bin/pnas.2022172118.sd01.xlsx Mmusculus 12 44081 44082 44078 44077 43895 43898 43891 43896 44080 44085 44079 43892"
## [166] "PMC7958240 /pmc/articles/PMC7958240/bin/pnas.2022172118.sd01.xlsx Rnorvegicus 4 43897 43894 44083 43892"
## [167] "PMC7958240 /pmc/articles/PMC7958240/bin/pnas.2022172118.sd01.xlsx Mmusculus 26 37135 39326 39692 40422 38231 40603 37865 38412 39508 37500 36951 39142 37681 36951 38777 38047 39873 38961 40787 40057 38596 37316 40238 37316 41153 41883"
## [168] "PMC7958240 /pmc/articles/PMC7958240/bin/pnas.2022172118.sd01.xlsx Mmusculus 26 40238 39326 37865 38596 38047 38231 39692 40057 40787 38961 36951 38777 37135 40422 40603 41153 38412 39508 37500 36951 39142 37681 41883 39873 37316 37316"
## [169] "PMC7958240 /pmc/articles/PMC7958240/bin/pnas.2022172118.sd01.xlsx Mmusculus 26 38231 38777 40057 40238 37316 39873 37865 38596 38961 36951 39326 39508 39692 40787 37316 38047 37135 40422 40603 41153 38412 37500 36951 39142 37681 41883"
## [170] "PMC7958240 /pmc/articles/PMC7958240/bin/pnas.2022172118.sd01.xlsx Mmusculus 26 37135 39326 39692 40422 38231 40603 37865 41153 38412 39508 37500 36951 39142 37681 41883 36951 38777 38047 39873 38961 40787 40057 38596 37316 40238 37316"
## [171] "PMC7931766 /pmc/articles/PMC7931766/bin/jitc-2020-001506supp002.xlsx Hsapiens 4 43891 43897 44075 44080"
## [172] "PMC7931766 /pmc/articles/PMC7931766/bin/jitc-2020-001506supp002.xlsx Hsapiens 26 43535 43719 43528 43531 43533 43529 43718 43710 43800 43527 43526 43711 43526 43532 43715 43717 43716 43720 43714 43709 43525 43712 43534 43722 43530 43525"
## [173] "PMC7931766 /pmc/articles/PMC7931766/bin/jitc-2020-001506supp002.xlsx Hsapiens 1 43525"
## [174] "PMC7931766 /pmc/articles/PMC7931766/bin/jitc-2020-001506supp002.xlsx Hsapiens 1 43896"
## [175] "PMC7928942 /pmc/articles/PMC7928942/bin/mmc3.xlsx Mmusculus 87 43891 43892 43899 44084 44084 44084 43900 43900 43900 43900 43900 43900 43900 43900 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44083 44082 44078 43901 43901 43901 43901 43901 43901 43901 43901 43901 43901 43901 43901 43901 43896 44077 44079 44079 44079 44079 44086 44086 43892 43892 43893 43893 43893 43893 43893 43893 43893 43893 43895 43895 43897 43897 43897 44088 44088 44085 44085 44085 44085 43898 43898 44075 44075 43891 43891 43891 44081 44081 44081 44080"
## [176] "PMC7925591 /pmc/articles/PMC7925591/bin/42003_2021_1788_MOESM4_ESM.xlsx Hsapiens 1 41883"
## [177] "PMC7956951 /pmc/articles/PMC7956951/bin/Table_2.xlsx Hsapiens 11 43897 43894 43891 43893 44081 43895 44086 44075 44078 43900 44079"
## [178] "PMC7956951 /pmc/articles/PMC7956951/bin/Table_3.xlsx Hsapiens 15 43897 43894 44076 44085 43891 43893 43895 43899 44086 44075 43900 44083 43892 44079 44077"
## [179] "PMC7956951 /pmc/articles/PMC7956951/bin/Table_4.xlsx Hsapiens 5 44086 44075 43900 44083 43892"
## [180] "PMC7956951 /pmc/articles/PMC7956951/bin/Table_5.xlsx Hsapiens 7 43897 43891 43893 43895 44075 43900 44083"
## [181] "PMC7956951 /pmc/articles/PMC7956951/bin/Table_6.xlsx Hsapiens 9 44076 43891 43893 43895 44086 44075 43900 44083 43892"
## [182] "PMC7956951 /pmc/articles/PMC7956951/bin/Table_7.xlsx Hsapiens 9 43894 44086 44075 44078 43900 44083 43892 44079 44080"
## [183] "PMC7956951 /pmc/articles/PMC7956951/bin/Table_8.xlsx Hsapiens 5 44086 44075 43900 44083 43892"
## [184] "PMC7956951 /pmc/articles/PMC7956951/bin/Table_9.xlsx Hsapiens 12 43897 43894 44085 43891 43893 43895 44086 44075 44083 43892 44079 44077"
## [185] "PMC7951976 /pmc/articles/PMC7951976/bin/pcbi.1008778.s001.xlsx Hsapiens 1 44078"
## [186] "PMC7951976 /pmc/articles/PMC7951976/bin/pcbi.1008778.s001.xlsx Hsapiens 2 44085 44080"
## [187] "PMC7951976 /pmc/articles/PMC7951976/bin/pcbi.1008778.s002.xlsx Hsapiens 2 44077 44078"
## [188] "PMC7951976 /pmc/articles/PMC7951976/bin/pcbi.1008778.s002.xlsx Hsapiens 3 44084 44085 44079"
## [189] "PMC7951976 /pmc/articles/PMC7951976/bin/pcbi.1008778.s002.xlsx Hsapiens 1 43895"
## [190] "PMC7921423 /pmc/articles/PMC7921423/bin/41467_2021_21614_MOESM12_ESM.xlsx Hsapiens 1 24432"
## [191] "PMC7917095 /pmc/articles/PMC7917095/bin/41438_2021_476_MOESM12_ESM.xlsx Athaliana 6 44077 44077 44076 44075 44107 44107"
## [192] "PMC7917095 /pmc/articles/PMC7917095/bin/41438_2021_476_MOESM7_ESM.xlsx Athaliana 24 44076 44075 44046 44046 44075 44075 44046 44046 44046 44046 44050 44050 44047 44107 44107 44106 44076 44047 44047 44050 44050 44107 44077 44077"
## [193] "PMC7917095 /pmc/articles/PMC7917095/bin/41438_2021_476_MOESM7_ESM.xlsx Athaliana 24 44076 44075 44046 44046 44075 44075 44046 44046 44046 44046 44050 44050 44047 44107 44107 44106 44076 44047 44047 44050 44050 44107 44077 44077"
## [194] "PMC7917095 /pmc/articles/PMC7917095/bin/41438_2021_476_MOESM8_ESM.xlsx Athaliana 6 44107 44077 44077 44076 44075 44107"
## [195] "PMC7913449 /pmc/articles/PMC7913449/bin/12864_2021_7430_MOESM4_ESM.xlsx Hsapiens 12 38596 37865 37500 38231 38961 41883 40422 40787 39326 39692 40057 41153"
## [196] "PMC7913449 /pmc/articles/PMC7913449/bin/12864_2021_7430_MOESM4_ESM.xlsx Hsapiens 14 38596 37865 37500 38231 38961 41883 40422 40787 39326 39692 40057 41153 37865 40057"
## [197] "PMC7913431 /pmc/articles/PMC7913431/bin/12920_2021_905_MOESM1_ESM.xlsx Hsapiens 2 44075 44080"
## [198] "PMC7953160 /pmc/articles/PMC7953160/bin/Table_2.XLSX Scerevisiae 1 42644"
## [199] "PMC7953160 /pmc/articles/PMC7953160/bin/Table_4.XLSX Scerevisiae 1 44105"
## [200] "PMC7910483 /pmc/articles/PMC7910483/bin/41398_2021_1263_MOESM7_ESM.xlsx Hsapiens 28 43800 43715 43710 43717 43711 43712 43527 43720 43719 43718 43533 43529 43713 43716 43528 43532 43714 43525 43534 43525 43709 43530 43531 43535 43723 43526 43526 43722"
## [201] "PMC7910483 /pmc/articles/PMC7910483/bin/41398_2021_1263_MOESM7_ESM.xlsx Hsapiens 28 43712 43716 43722 43526 43800 43713 43711 43709 43531 43718 43527 43535 43534 43715 43720 43525 43719 43533 43530 43723 43714 43529 43525 43528 43717 43710 43532 43526"
## [202] "PMC7910483 /pmc/articles/PMC7910483/bin/41398_2021_1263_MOESM7_ESM.xlsx Hsapiens 28 43711 43528 43714 43800 43527 43718 43525 43719 43712 43723 43717 43709 43533 43526 43529 43722 43526 43716 43530 43532 43534 43713 43535 43710 43531 43715 43720 43525"
## [203] "PMC7910483 /pmc/articles/PMC7910483/bin/41398_2021_1263_MOESM7_ESM.xlsx Hsapiens 28 43709 43716 43715 43526 43529 43525 43722 43535 43531 43533 43712 43718 43719 43532 43714 43711 43528 43717 43534 43710 43800 43527 43723 43530 43526 43525 43720 43713"
## [204] "PMC7910483 /pmc/articles/PMC7910483/bin/41398_2021_1263_MOESM7_ESM.xlsx Hsapiens 28 43722 43525 43535 43713 43723 43710 43709 43716 43530 43719 43532 43533 43711 43714 43800 43528 43534 43720 43526 43525 43531 43712 43529 43526 43527 43717 43718 43715"
## [205] "PMC7910483 /pmc/articles/PMC7910483/bin/41398_2021_1263_MOESM7_ESM.xlsx Hsapiens 28 43528 43713 43527 43535 43722 43714 43709 43718 43716 43532 43531 43711 43800 43526 43715 43533 43525 43525 43723 43534 43720 43717 43719 43712 43530 43529 43526 43710"
## [206] "PMC7910482 /pmc/articles/PMC7910482/bin/41467_2021_21612_MOESM3_ESM.xlsx Hsapiens 1 40603"
## [207] "PMC7910459 /pmc/articles/PMC7910459/bin/41467_2021_21478_MOESM6_ESM.xlsx Hsapiens 1 41883"
## [208] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_2.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [209] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_2.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [210] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_2.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [211] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_2.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [212] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_2.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [213] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_2.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [214] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_2.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [215] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_4.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [216] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_4.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [217] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_4.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [218] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_4.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [219] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_4.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [220] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_4.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [221] "PMC7959850 /pmc/articles/PMC7959850/bin/DataSheet_4.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [222] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc2.xls Mmusculus 27 44084 44086 44080 44083 44076 44081 44075 44088 44085 43895 43894 43897 43896 43891 43893 43892 43899 43898 44089 43900 43892 44082 44079 44078 44077 43891 43901"
## [223] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc2.xls Mmusculus 15 2020/09/10 2020/09/06 2020/09/09 2020/09/11 2020/03/04 2020/03/01 2020/03/03 2020/03/08 2020/03/10 2020/09/08 2020/09/05 2020/09/04 2020/09/03 2020/03/01 2020/03/11"
## [224] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc2.xls Mmusculus 3 2020/09/09 2020/09/08 2020/09/05"
## [225] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc2.xls Mmusculus 14 2020/09/10 2020/09/09 2020/09/11 2020/03/04 2020/03/01 2020/03/03 2020/03/09 2020/03/08 2020/03/10 2020/09/05 2020/09/04 2020/09/03 2020/03/01 2020/03/11"
## [226] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc2.xls Mmusculus 12 44084 44083 43894 43891 43893 43898 43900 44079 44078 44077 43891 43901"
## [227] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc3.xls Mmusculus 1 2020/03/03"
## [228] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc3.xls Mmusculus 1 43893"
## [229] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc4.xls Mmusculus 1 2020/09/01"
## [230] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc4.xls Mmusculus 2 2020/03/09 2020/09/03"
## [231] "PMC7940259 /pmc/articles/PMC7940259/bin/mmc4.xls Mmusculus 1 43897"
## [232] "PMC7945945 /pmc/articles/PMC7945945/bin/Table_3.xlsx Hsapiens 24 43533 43716 43525 43528 43530 43800 43527 43709 43525 43715 43719 43712 43717 43526 43526 43534 43718 43713 43532 43531 43711 43714 43710 43529"
## [233] "PMC7945594 /pmc/articles/PMC7945594/bin/Table_3.xlsx Hsapiens 34 40787 40787 39692 38231 38231 39692 38961 38961 39326 39692 37135 39326 40422 40057 40057 42248 38961 40057 37500 40787 38961 38961 37500 40057 40422 40787 39326 37865 39326 41153 37500 38231 37500 37500"
## [234] "PMC7945594 /pmc/articles/PMC7945594/bin/Table_3.xlsx Hsapiens 15 39326 41153 37500 40787 38961 38596 38961 42248 38596 40422 38231 40057 37865 37500 41883"
## [235] "PMC7944992 /pmc/articles/PMC7944992/bin/Table_1.xls Hsapiens 28 2020/03/08 2020/09/09 2020/09/01 2020/09/01 2020/03/02 2020/03/03 2020/03/01 2020/09/05 2020/03/06 2020/03/07 2020/03/09 2020/03/04 2020/09/03 2020/03/10 2020/03/01 2020/09/15 2020/03/05 2020/09/07 2020/12/01 2020/09/11 2020/03/11 2020/09/14 2020/09/04 2020/03/02 2020/09/08 2020/09/10 2020/09/02 2020/09/12"
## [236] "PMC7943886 /pmc/articles/PMC7943886/bin/Table_1.xlsx Hsapiens 1 43349"
## [237] "PMC7903607 /pmc/articles/PMC7903607/bin/12911_2021_1387_MOESM2_ESM.xlsx Hsapiens 11 41706 41699 41701 41974 41890 41699 41888 41705 41891 41893 41701"
## [238] "PMC7935315 /pmc/articles/PMC7935315/bin/pbio.3001138.s027.xlsx Hsapiens 1 41153"
## [239] "PMC7935315 /pmc/articles/PMC7935315/bin/pbio.3001138.s030.xlsx Hsapiens 1 40238"
## [240] "PMC7935315 /pmc/articles/PMC7935315/bin/pbio.3001138.s032.xlsx Hsapiens 1 40238"
## [241] "PMC7935315 /pmc/articles/PMC7935315/bin/pbio.3001138.s033.xlsx Hsapiens 24 38231 38047 37316 37681 38961 37316 39873 41883 38596 37226 36951 37865 40422 40057 37500 39692 38777 39326 39142 38412 39508 40787 37135 40603"
## [242] "PMC7902657 /pmc/articles/PMC7902657/bin/41467_2021_21409_MOESM6_ESM.xls Mmusculus 2 43714 43712"
## [243] "PMC7902657 /pmc/articles/PMC7902657/bin/41467_2021_21409_MOESM7_ESM.xls Mmusculus 4 43714 43712 43714 43714"
## [244] "PMC7902657 /pmc/articles/PMC7902657/bin/41467_2021_21409_MOESM8_ESM.xls Mmusculus 2 43716 43718"
## [245] "PMC7902657 /pmc/articles/PMC7902657/bin/41467_2021_21409_MOESM9_ESM.xls Mmusculus 5 43716 43716 43716 43716 43718"
## [246] "PMC7902657 /pmc/articles/PMC7902657/bin/41467_2021_21409_MOESM9_ESM.xls Mmusculus 35 43716 43716 43716 43716 43716 43718 43716 43718 43718 43716 43716 43718 43718 43716 43716 43716 43716 43716 43718 43716 43716 43716 43716 43718 43716 43716 43716 43716 43716 43716 43716 43716 43716 43716 43716"
## [247] "PMC7937961 /pmc/articles/PMC7937961/bin/Table_3.xlsx Hsapiens 3 40057 40057 40057"
## [248] "PMC7937961 /pmc/articles/PMC7937961/bin/Table_3.xlsx Hsapiens 2 44265 44448"
## [249] "PMC7937961 /pmc/articles/PMC7937961/bin/Table_3.xlsx Hsapiens 1 44261"
## [250] "PMC7937961 /pmc/articles/PMC7937961/bin/Table_4.xlsx Hsapiens 6 44256 44260 44265 44259 44266 44258"
## [251] "PMC7937961 /pmc/articles/PMC7937961/bin/Table_4.xlsx Hsapiens 1 44261"
## [252] "PMC7900196 /pmc/articles/PMC7900196/bin/42003_2021_1756_MOESM5_ESM.xlsx Mmusculus 24 42613 42619 42620 42622 42616 42439 42615 42433 42436 42614 42429 42435 42431 42429 42627 42434 42432 42437 42618 42623 42621 42617 42430 42430"
## [253] "PMC7974522 /pmc/articles/PMC7974522/bin/jcav12p2151s2.xlsx Hsapiens 2 44531 44266"
## [254] "PMC7974522 /pmc/articles/PMC7974522/bin/jcav12p2151s2.xlsx Hsapiens 2 43800 43535"
## [255] "PMC7974522 /pmc/articles/PMC7974522/bin/jcav12p2151s2.xlsx Hsapiens 1 43532"
## [256] "PMC7974522 /pmc/articles/PMC7974522/bin/jcav12p2151s2.xlsx Hsapiens 1 43532"
## [257] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_1.XLSX Hsapiens 1 36951"
## [258] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_1.XLSX Hsapiens 1 36951"
## [259] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_1.XLSX Hsapiens 1 36951"
## [260] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_1.XLSX Hsapiens 1 36951"
## [261] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_1.XLSX Hsapiens 9 37681 40603 38047 39692 38777 40603 40787 37681 37226"
## [262] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_1.XLSX Hsapiens 6 38047 37226 38961 40057 40057 38596"
## [263] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_1.XLSX Hsapiens 9 37681 39692 38777 40603 38961 40057 36951 36951 40057"
## [264] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_1.XLSX Hsapiens 13 37681 40603 40603 40787 37681 36951 40057 36951 38596 41518 40057 40057 38596"
## [265] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_3.xlsx Hsapiens 18 37316 36951 36951 40603 40787 38961 38596 40787 40057 40057 36951 41153 38961 37500 37500 37865 39142 38961"
## [266] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_4.XLSX Hsapiens 1 36951"
## [267] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_4.XLSX Hsapiens 12 40603 40057 40057 37681 38961 38961 36951 36951 36951 36951 39508 37316"
## [268] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_4.XLSX Hsapiens 13 40603 40057 37681 38961 38961 36951 39508 40057 40057 40238 40238 36951 38961"
## [269] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_4.XLSX Hsapiens 13 40603 40057 36951 36951 37316 36951 38596 38777 39508 37681 40787 37500 36951"
## [270] "PMC7933519 /pmc/articles/PMC7933519/bin/Table_6.xlsx Hsapiens 1 40787"
## [271] "PMC7895368 /pmc/articles/PMC7895368/bin/pone.0247233.s005.xlsx Hsapiens 14 43894 43900 43895 43893 43901 43892 43896 43892 44166 43899 43897 43891 43898 43891"
## [272] "PMC7895368 /pmc/articles/PMC7895368/bin/pone.0247233.s005.xlsx Hsapiens 14 43891 43898 43892 43891 43899 44166 43895 43892 43893 43896 43894 43901 43900 43897"
## [273] "PMC7895368 /pmc/articles/PMC7895368/bin/pone.0247233.s005.xlsx Hsapiens 14 43894 43891 43901 43896 43893 43897 43899 43891 43892 43898 43900 43892 43895 44166"
## [274] "PMC7895368 /pmc/articles/PMC7895368/bin/pone.0247233.s005.xlsx Hsapiens 14 43891 43898 43892 43891 43899 43901 43894 43897 43896 44166 43895 43892 43893 43900"
## [275] "PMC7931689 /pmc/articles/PMC7931689/bin/DataSheet_1.xlsx Hsapiens 1 43354"
## [276] "PMC7931689 /pmc/articles/PMC7931689/bin/DataSheet_1.xlsx Hsapiens 1 43354"
## [277] "PMC7931689 /pmc/articles/PMC7931689/bin/DataSheet_1.xlsx Hsapiens 1 43354"
## [278] "PMC7931689 /pmc/articles/PMC7931689/bin/DataSheet_1.xlsx Hsapiens 3 43163 43352 43160"
## [279] "PMC7930499 /pmc/articles/PMC7930499/bin/Table_2.XLSX Hsapiens 27 44076 43896 44083 44081 44085 44077 43897 43895 43898 44082 44080 44079 44084 43899 43894 44078 43891 43892 43901 43891 44075 44088 43893 44166 43892 44086 43900"
## [280] "PMC7924761 /pmc/articles/PMC7924761/bin/pgen.1009338.s008.xlsx Dmelanogaster 5 44078 44079 44076 44075 44166"
## [281] "PMC7924761 /pmc/articles/PMC7924761/bin/pgen.1009338.s008.xlsx Dmelanogaster 5 44078 44079 44076 44075 44166"
## [282] "PMC7924761 /pmc/articles/PMC7924761/bin/pgen.1009338.s008.xlsx Dmelanogaster 5 44078 44079 44076 44075 44166"
## [283] "PMC7924761 /pmc/articles/PMC7924761/bin/pgen.1009338.s008.xlsx Dmelanogaster 5 44078 44079 44076 44075 44166"
## [284] "PMC7905234 /pmc/articles/PMC7905234/bin/mmc2.xlsx Hsapiens 28 44085 43892 44083 44076 43891 43892 43891 44079 44089 43900 44075 43893 44081 43896 43901 44086 43898 43894 44166 44075 44082 44084 43897 43895 44088 43899 44077 44078"
## [285] "PMC7892573 /pmc/articles/PMC7892573/bin/41467_2021_21365_MOESM10_ESM.xlsx Hsapiens 13 37500 40057 39326 38961 38231 39692 37316 40422 42248 40787 38596 37865 37135"
## [286] "PMC7892573 /pmc/articles/PMC7892573/bin/41467_2021_21365_MOESM16_ESM.xlsx Hsapiens 3 42248 38596 37135"
## [287] "PMC7892573 /pmc/articles/PMC7892573/bin/41467_2021_21365_MOESM16_ESM.xlsx Hsapiens 1 37500"
## [288] "PMC7892573 /pmc/articles/PMC7892573/bin/41467_2021_21365_MOESM5_ESM.xlsx Hsapiens 16 42795 42795 42801 42800 42800 42802 42980 42800 42795 42795 42985 43070 42802 42797 42795 42795"
## [289] "PMC7892572 /pmc/articles/PMC7892572/bin/41467_2021_21300_MOESM5_ESM.xlsx Ggallus 8 40422 40787 40057 37865 37865 37865 37865 38961"
## [290] "PMC7925823 /pmc/articles/PMC7925823/bin/Table_1.xlsx Hsapiens 1 43535"
## [291] "PMC7886901 /pmc/articles/PMC7886901/bin/41467_2021_21357_MOESM6_ESM.xls Mmusculus 2 44082 44075"
## [292] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-4.xlsx Mmusculus 54 44081 44076 44078 43895 44081 44076 43895 43895 44081 44076 44075 43895 44081 43897 43892 43891 44076 43891 44076 44089 44089 44083 43895 44081 44080 44082 44084 43892 44078 43900 43891 43892 44089 44078 44076 44083 43893 43899 44080 43900 43895 44089 43897 43898 44081 44078 44083 44081 44080 43900 44084 43895 43897 43892"
## [293] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-4.xlsx Mmusculus 50 44081 44076 44078 43895 44081 44076 43895 43895 44081 44076 44075 43895 44081 43897 43892 43891 44076 43891 44076 44083 43895 44081 44080 44082 44084 43892 44078 43900 43891 43892 44078 44076 44083 43893 43899 44080 43900 43895 43897 43898 44081 44078 44083 44081 44080 43900 44084 43895 43897 43892"
## [294] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-4.xlsx Mmusculus 49 44081 44076 43891 44078 43895 44081 44078 44076 44081 44076 43895 43895 44081 44076 43895 43892 43891 44076 43892 44076 44083 43895 44081 44080 44082 44084 43892 44078 43900 43891 43892 44089 44078 44076 43893 44082 43899 44081 43892 43891 43895 44084 43900 44078 44082 43895 44083 44089 43892"
## [295] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-4.xlsx Mmusculus 47 44081 44076 43891 44078 43895 44081 44078 44076 44081 44076 43895 43895 44081 44076 43895 43892 43891 44076 43892 44076 44083 43895 44081 44080 44082 44084 43892 44078 43900 43891 43892 44078 44076 43893 44082 43899 44081 43892 43891 43895 44084 43900 44078 44082 43895 44083 43892"
## [296] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-4.xlsx Mmusculus 57 44076 44076 43891 44076 43891 44076 44078 44076 44081 44076 43895 44076 44076 44076 44075 43895 44076 44076 44076 44076 44076 44076 44089 44076 44076 44078 44076 44083 43893 43899 44080 43900 43895 44089 43897 43898 44081 44078 44076 43893 44082 43899 44081 43892 43891 43895 44084 43900 44076 43893 43899 44078 44083 44089 44075 43891 44085"
## [297] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-4.xlsx Mmusculus 54 44076 44076 43891 44076 43891 44076 44078 44076 44081 44076 43895 44076 44076 44076 44075 43895 44076 44076 44076 44076 44076 44076 44076 44076 44078 44076 44083 43893 43899 44080 43900 43895 43897 43898 44081 44078 44076 43893 44082 43899 44081 43892 43891 43895 44084 43900 44076 43893 43899 44078 44083 44075 43891 44085"
## [298] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-4.xlsx Mmusculus 37 44076 43891 44076 44076 44081 43897 43895 44076 43891 43892 44076 44089 44076 44078 44083 44081 44080 43900 44084 43895 43897 43892 44078 44082 43895 44083 44089 43892 44076 43893 43899 44078 44083 44089 44075 43891 44085"
## [299] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-4.xlsx Mmusculus 34 44076 43891 44076 44076 44081 43897 43895 44076 43891 43892 44076 44076 44078 44083 44081 44080 43900 44084 43895 43897 43892 44078 44082 43895 44083 43892 44076 43893 43899 44078 44083 44075 43891 44085"
## [300] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-5.xlsx Mmusculus 18 44085 43892 44080 44075 43896 43898 44082 43895 43891 44084 43897 44076 43892 44081 44089 43893 44078 43899"
## [301] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-5.xlsx Mmusculus 15 43895 44081 44084 44085 43892 43897 43891 44075 43898 43896 43892 44089 44082 44076 44080"
## [302] "PMC7937391 /pmc/articles/PMC7937391/bin/NIHMS1672405-supplement-5.xlsx Mmusculus 14 44085 43891 44084 44076 43898 43892 44089 44081 43897 44075 43896 44082 43895 43892"
## [303] "PMC7957197 /pmc/articles/PMC7957197/bin/JCMM-25-2918-s002.xlsx Hsapiens 1 43529"
## [304] "PMC7986194 /pmc/articles/PMC7986194/bin/MEC-30-938-s002.xlsx Dmelanogaster 24 Harbison, S. T., McCoy, L. J., & Mackay, T. F. (2013). Genome-wide association study of sleep in Drosophila melanogaster. BMC Genomics, 14, 281. doi:10.1186/1471-2164-14-281"
## [305] "PMC7910251 /pmc/articles/PMC7910251/bin/11060_2020_3694_MOESM3_ESM.xlsx Hsapiens 5 43891 43891 43891 43891 43891"
## [306] "PMC7910251 /pmc/articles/PMC7910251/bin/11060_2020_3694_MOESM3_ESM.xlsx Hsapiens 3 44084 44085 44078"
## [307] "PMC7910251 /pmc/articles/PMC7910251/bin/11060_2020_3694_MOESM3_ESM.xlsx Hsapiens 4 43891 43891 44084 44078"
## [308] "PMC7906164 /pmc/articles/PMC7906164/bin/aging-13-202417-s002.xls Hsapiens 2 2020/03/01 2020/09/09"
## [309] "PMC7906164 /pmc/articles/PMC7906164/bin/aging-13-202417-s003.xls Hsapiens 1 44083"
## [310] "PMC7906164 /pmc/articles/PMC7906164/bin/aging-13-202417-s003.xls Hsapiens 1 44081"
## [311] "PMC7906164 /pmc/articles/PMC7906164/bin/aging-13-202417-s003.xls Hsapiens 2 43891 43898"
## [312] "PMC7906164 /pmc/articles/PMC7906164/bin/aging-13-202417-s003.xls Hsapiens 1 44085"
## [313] "PMC7892346 /pmc/articles/PMC7892346/bin/41388_2020_1614_MOESM3_ESM.xlsx Hsapiens 4 43891 44081 43894 43894"
## [314] "PMC7892346 /pmc/articles/PMC7892346/bin/41388_2020_1614_MOESM3_ESM.xlsx Hsapiens 2 43896 44081"
## [315] "PMC7892341 /pmc/articles/PMC7892341/bin/41388_2020_1606_MOESM3_ESM.xlsx Hsapiens 6 40057 39326 39326 40787 40057 37500"
## [316] "PMC7892341 /pmc/articles/PMC7892341/bin/41388_2020_1606_MOESM3_ESM.xlsx Hsapiens 1 39326"
## [317] "PMC7892341 /pmc/articles/PMC7892341/bin/41388_2020_1606_MOESM3_ESM.xlsx Hsapiens 7 40238 37135 38777 37865 37681 38961 38231"
## [318] "PMC7892341 /pmc/articles/PMC7892341/bin/41388_2020_1606_MOESM3_ESM.xlsx Hsapiens 1 39326"
## [319] "PMC7892341 /pmc/articles/PMC7892341/bin/41388_2020_1606_MOESM3_ESM.xlsx Hsapiens 7 39508 39508 40057 38047 39508 40057 39508"
## [320] "PMC7906150 /pmc/articles/PMC7906150/bin/aging-13-202331-s002.xlsx Mmusculus 1 43893"
## [321] "PMC7948421 /pmc/articles/PMC7948421/bin/mmc1.xlsx Hsapiens 1 44081"
## [322] "PMC7610462 /pmc/articles/PMC7610462/bin/EMS118385-supplement-Supplementary_Tables.xlsx Ggallus 15 42065 42073 42073 42248 42063 42063 42063 42063 42063 42063 42063 42063 42068 42063 42063"
## [323] "PMC7610462 /pmc/articles/PMC7610462/bin/EMS118385-supplement-Supplementary_Tables.xlsx Ggallus 4 42063 42063 42063 42063"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 Ggallus Hsapiens Mmusculus
## 4 23 7 242 44
## Rnorvegicus Scerevisiae
## 1 2par(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##
## PMC7610462 PMC7886901 PMC7892341 PMC7892346 PMC7892572 PMC7892573 PMC7895368
## 2 1 5 2 1 4 4
## PMC7900196 PMC7902657 PMC7903607 PMC7905234 PMC7906150 PMC7906164 PMC7910251
## 1 5 1 1 1 5 3
## PMC7910459 PMC7910482 PMC7910483 PMC7913431 PMC7913449 PMC7917095 PMC7921423
## 1 1 6 1 2 4 1
## PMC7924761 PMC7925591 PMC7925823 PMC7928942 PMC7930499 PMC7931689 PMC7931766
## 4 1 1 1 1 4 4
## PMC7932549 PMC7933180 PMC7933519 PMC7934467 PMC7934504 PMC7935315 PMC7935873
## 1 1 14 1 3 4 4
## PMC7937391 PMC7937961 PMC7939296 PMC7939520 PMC7940259 PMC7940623 PMC7941712
## 11 5 1 4 10 15 5
## PMC7942004 PMC7942016 PMC7943886 PMC7944992 PMC7945594 PMC7945945 PMC7946432
## 3 2 1 1 2 1 5
## PMC7946903 PMC7948421 PMC7951976 PMC7953160 PMC7955039 PMC7956951 PMC7957197
## 5 1 5 2 2 8 1
## PMC7958140 PMC7958240 PMC7958471 PMC7959850 PMC7968334 PMC7968368 PMC7973040
## 2 8 2 14 1 2 2
## PMC7973504 PMC7974522 PMC7980388 PMC7980453 PMC7981925 PMC7981997 PMC7982637
## 15 4 1 2 1 1 1
## PMC7982650 PMC7984841 PMC7986194 PMC7987945 PMC7990797 PMC7994849 PMC7999279
## 64 9 1 3 2 1 1summary(as.numeric(DIST))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.000 1.000 2.000 4.195 4.000 64.000hist(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
## 71 PMC7982650 64
## 41 PMC7940623 15
## 64 PMC7973504 15
## 31 PMC7933519 14
## 60 PMC7959850 14
## 36 PMC7937391 11
## 40 PMC7940259 10
## 72 PMC7984841 9
## 55 PMC7956951 8
## 58 PMC7958240 8
## 17 PMC7910483 6
## 3 PMC7892341 5
## 9 PMC7902657 5
## 13 PMC7906164 5
## 37 PMC7937961 5
## 42 PMC7941712 5
## 49 PMC7946432 5
## 50 PMC7946903 5
## 52 PMC7951976 5
## 6 PMC7892573 4MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES## [1] "PMC7982650"# 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## PMC7610462 PMC7886901 PMC7892341 PMC7892346 PMC7892572 PMC7892573 PMC7895368
## 19 2 22 6 8 33 56
## PMC7900196 PMC7902657 PMC7903607 PMC7905234 PMC7906150 PMC7906164 PMC7910251
## 24 48 11 28 1 7 12
## PMC7910459 PMC7910482 PMC7910483 PMC7913431 PMC7913449 PMC7917095 PMC7921423
## 1 1 168 2 26 60 1
## PMC7924761 PMC7925591 PMC7925823 PMC7928942 PMC7930499 PMC7931689 PMC7931766
## 20 1 1 87 27 6 32
## PMC7932549 PMC7933180 PMC7933519 PMC7934467 PMC7934504 PMC7935315 PMC7935873
## 1 18 99 19 7 27 16
## PMC7937391 PMC7937961 PMC7939296 PMC7939520 PMC7940259 PMC7940623 PMC7941712
## 429 13 3 52 77 20 18
## PMC7942004 PMC7942016 PMC7943886 PMC7944992 PMC7945594 PMC7945945 PMC7946432
## 61 13 1 28 49 24 17
## PMC7946903 PMC7948421 PMC7951976 PMC7953160 PMC7955039 PMC7956951 PMC7957197
## 50 1 9 2 2 73 1
## PMC7958140 PMC7958240 PMC7958471 PMC7959850 PMC7968334 PMC7968368 PMC7973040
## 53 172 6 392 1 14 4
## PMC7973504 PMC7974522 PMC7980388 PMC7980453 PMC7981925 PMC7981997 PMC7982637
## 78 6 2 77 13 14 1
## PMC7982650 PMC7984841 PMC7986194 PMC7987945 PMC7990797 PMC7994849 PMC7999279
## 275 36 24 26 30 1 2hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
head(NERR_DF,20)## NERR
## PMC7937391 429
## PMC7959850 392
## PMC7982650 275
## PMC7958240 172
## PMC7910483 168
## PMC7933519 99
## PMC7928942 87
## PMC7973504 78
## PMC7940259 77
## PMC7980453 77
## PMC7956951 73
## PMC7942004 61
## PMC7917095 60
## PMC7895368 56
## PMC7958140 53
## PMC7939520 52
## PMC7946903 50
## PMC7945594 49
## PMC7902657 48
## PMC7984841 36MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR## [1] "PMC7937391"Journals affected
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
### JSON PARSING is more reliable than XML
ARTICLES <- esummary( GENELIST_ERROR_ARTICLES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA$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] 48par(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] "7982650"
##
## $result$`7982650`
## $result$`7982650`$uid
## [1] "7982650"
##
## $result$`7982650`$pubdate
## [1] "2021 Mar 8"
##
## $result$`7982650`$epubdate
## [1] "2021 Mar 8"
##
## $result$`7982650`$printpubdate
## [1] ""
##
## $result$`7982650`$source
## [1] "Front Genet"
##
## $result$`7982650`$authors
## name authtype
## 1 Ye X Author
## 2 Wei J Author
## 3 Yue M Author
## 4 Wang Y Author
## 5 Chen H Author
## 6 Zhang Y Author
## 7 Wang Y Author
## 8 Zhang M Author
## 9 Huang P Author
## 10 Yu R Author
##
## $result$`7982650`$title
## [1] "Leveraging Single-Cell RNA-seq Data to Uncover the Association Between Cell Type and Chronic Liver Diseases"
##
## $result$`7982650`$volume
## [1] "12"
##
## $result$`7982650`$issue
## [1] ""
##
## $result$`7982650`$pages
## [1] "637322"
##
## $result$`7982650`$articleids
## idtype value
## 1 pmid 33763117
## 2 doi 10.3389/fgene.2021.637322
## 3 pmcid PMC7982650
##
## $result$`7982650`$fulljournalname
## [1] "Frontiers in Genetics"
##
## $result$`7982650`$sortdate
## [1] "2021/03/08 00:00"
##
## $result$`7982650`$pmclivedate
## [1] "2021/03/23"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] "7937391"
##
## $result$`7937391`
## $result$`7937391`$uid
## [1] "7937391"
##
## $result$`7937391`$pubdate
## [1] "2021 Feb 9"
##
## $result$`7937391`$epubdate
## [1] ""
##
## $result$`7937391`$printpubdate
## [1] "2021 Feb 9"
##
## $result$`7937391`$source
## [1] "Cell Rep"
##
## $result$`7937391`$authors
## name authtype
## 1 Yang HS Author
## 2 Onos KD Author
## 3 Choi K Author
## 4 Keezer KJ Author
## 5 Skelly DA Author
## 6 Carter GW Author
## 7 Howell GR Author
##
## $result$`7937391`$title
## [1] "Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer’s disease"
##
## $result$`7937391`$volume
## [1] "34"
##
## $result$`7937391`$issue
## [1] "6"
##
## $result$`7937391`$pages
## [1] "108739"
##
## $result$`7937391`$articleids
## idtype value
## 1 pmid 33567283
## 2 doi 10.1016/j.celrep.2021.108739
## 3 pmcid PMC7937391
## 4 MID NIHMS1672405
##
## $result$`7937391`$fulljournalname
## [1] "Cell reports"
##
## $result$`7937391`$sortdate
## [1] "2021/02/09 00:00"
##
## $result$`7937391`$pmclivedate
## [1] "2021/03/07"Trend info
TODO: To plot the trend over the past 6 months.
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 3.6.3 (2020-02-29)
## 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
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.6 knitr_1.31 magrittr_2.0.1 R6_2.5.0
## [5] rlang_0.4.10 highr_0.8 stringr_1.4.0 tools_3.6.3
## [9] xfun_0.22 jquerylib_0.1.3 htmltools_0.5.1.1 yaml_2.2.1
## [13] digest_0.6.27 assertthat_0.2.1 sass_0.3.1 bitops_1.0-6
## [17] RCurl_1.98-1.3 evaluate_0.14 rmarkdown_2.7 stringi_1.5.3
## [21] compiler_3.6.3 bslib_0.2.4 cellranger_1.1.0 XML_3.99-0.3