Gene Name Error Monthly Dashboard
Mark Ziemann
2026-07-31
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="2026/3"
#2024-06Let’s see how many PMC IDs we have in the past month.
QUERY ='((genom*[Title/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 4000## Retrieving UIDs 4001 to 4500pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 4205writeLines(pmc,con="pmc.txt")Run the screen
Now run the bash script. As PMC has changed and restricts scraping journal articles, it is best to use the dedicated utility called pygetpapers for the download.
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] 90984NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 1503GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 742NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 390ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 207GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC13034595" "PMC13035081" "PMC12891060" "PMC13034653" "PMC12698805"
## [6] "PMC11850471" "PMC10060313" "PMC13032165" "PMC13031693" "PMC13030874"
## [11] "PMC13025642" "PMC13023209" "PMC13021997" "PMC13019979" "PMC13018755"
## [16] "PMC13014123" "PMC13016824" "PMC13009199" "PMC13010944" "PMC13011747"
## [21] "PMC13011774" "PMC13006575" "PMC13005615" "PMC13004839" "PMC13003602"
## [26] "PMC13004596" "PMC13004595" "PMC13003292" "PMC12999485" "PMC13001983"
## [31] "PMC13000003" "PMC13000244" "PMC12999466" "PMC12995690" "PMC12998166"
## [36] "PMC12996886" "PMC12993451" "PMC12992800" "PMC12992822" "PMC12991876"
## [41] "PMC12987951" "PMC12988094" "PMC12987736" "PMC12984511" "PMC12985480"
## [46] "PMC12987650" "PMC12982611" "PMC12985386" "PMC12987568" "PMC12979158"
## [51] "PMC12979829" "PMC12978397" "PMC12978698" "PMC12978544" "PMC12977612"
## [56] "PMC12975130" "PMC12974471" "PMC12971484" "PMC12968393" "PMC12965172"
## [61] "PMC12964230" "PMC12965291" "PMC12963367" "PMC12962868" "PMC12961773"
## [66] "PMC12960846" "PMC12960819" "PMC12959415" "PMC12957397" "PMC12957838"
## [71] "PMC12957787" "PMC11897779" "PMC12953882" "PMC12953642" "PMC12956043"
## [76] "PMC12953866" "PMC12952131" "PMC12951959" "PMC12948414" "PMC12948831"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 80ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.2051282Look 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] "PMC13034595 PMC_DL/PMC13034595/supplementaryfiles/13073_2026_1611_MOESM2_ESM.xlsx Hsapiens 2 45717 45718"
## [2] "PMC13034595 PMC_DL/PMC13034595/supplementaryfiles/13073_2026_1611_MOESM2_ESM.xlsx Hsapiens 1 45717"
## [3] "PMC13034595 PMC_DL/PMC13034595/supplementaryfiles/13073_2026_1611_MOESM2_ESM.xlsx Hsapiens 1 45718"
## [4] "PMC13035081 zip/Suppl_Data_file1.xlsx Drerio 1 45717"
## [5] "PMC12891060 PMC_DL/PMC12891060/supplementaryfiles/13402_2026_1173_MOESM9_ESM.xlsx Hsapiens 3 39692 38231 40057"
## [6] "PMC13034653 PMC_DL/PMC13034653/supplementaryfiles/NIHMS2151702-supplement-2.xlsx Hsapiens 26 44628 44626 44812 44810 44819 44807 44625 44631 44816 44811 44624 44629 44622 44809 44806 44818 44623 44896 44627 44805 44815 44621 44808 44630 44814 44813"
## [7] "PMC12698805 PMC_DL/PMC12698805/supplementaryfiles/13402_2025_1097_MOESM3_ESM.xlsx Hsapiens 112 39326 39326 39326 39326 37135 37135 37135 37135 37500 37500 37500 37500 38596 38596 38596 38596 38231 38231 38231 38231 42248 42248 42248 42248 38777 38777 38777 38777 40057 40057 40057 40057 38961 38961 38961 38961 39692 39692 39692 39692 37226 37226 37226 37226 37316 37316 37316 37316 38412 38412 38412 38412 37316 37316 37316 37316 36951 36951 36951 36951 40787 40787 40787 40787 37865 37865 37865 37865 38047 38047 38047 38047 36951 36951 36951 36951 39142 39142 39142 39142 39873 39873 39873 39873 37681 37681 37681 37681 41153 41153 41153 41153 40422 40422 40422 40422 40238 40238 40238 40238 39508 39508 39508 39508 41883 41883 41883 41883 40603 40603 40603 40603"
## [8] "PMC12698805 PMC_DL/PMC12698805/supplementaryfiles/13402_2025_1097_MOESM3_ESM.xlsx Hsapiens 112 39326 39326 39326 39326 37135 37135 37135 37135 37500 37500 37500 37500 38596 38596 38596 38596 38231 38231 38231 38231 42248 42248 42248 42248 38777 38777 38777 38777 40057 40057 40057 40057 38961 38961 38961 38961 39692 39692 39692 39692 37226 37226 37226 37226 37316 37316 37316 37316 38412 38412 38412 38412 37316 37316 37316 37316 36951 36951 36951 36951 40787 40787 40787 40787 37865 37865 37865 37865 38047 38047 38047 38047 36951 36951 36951 36951 39142 39142 39142 39142 39873 39873 39873 39873 37681 37681 37681 37681 41153 41153 41153 41153 40422 40422 40422 40422 40238 40238 40238 40238 39508 39508 39508 39508 41883 41883 41883 41883 40603 40603 40603 40603"
## [9] "PMC12698805 PMC_DL/PMC12698805/supplementaryfiles/13402_2025_1097_MOESM3_ESM.xlsx Hsapiens 2 40422 39508"
## [10] "PMC12698805 PMC_DL/PMC12698805/supplementaryfiles/13402_2025_1097_MOESM3_ESM.xlsx Hsapiens 2 40422 39508"
## [11] "PMC12698805 PMC_DL/PMC12698805/supplementaryfiles/13402_2025_1097_MOESM3_ESM.xlsx Hsapiens 1 37500"
## [12] "PMC12698805 PMC_DL/PMC12698805/supplementaryfiles/13402_2025_1097_MOESM3_ESM.xlsx Hsapiens 1 37500"
## [13] "PMC11850471 PMC_DL/PMC11850471/supplementaryfiles/13402_2024_978_MOESM1_ESM.xlsx Mmusculus 4 44450 44448 44256 44448"
## [14] "PMC11850471 PMC_DL/PMC11850471/supplementaryfiles/13402_2024_978_MOESM1_ESM.xlsx Mmusculus 3 44450 44256 44444"
## [15] "PMC10060313 PMC_DL/PMC10060313/supplementaryfiles/13402_2022_758_MOESM5_ESM.xlsx Hsapiens 6 44815 44621 44808 44809 44807 44810"
## [16] "PMC13032165 PMC_DL/PMC13032165/supplementaryfiles/TPG2-19-e70227-s006.xlsx Athaliana 16 38200 38565 38565 38565 39661 37104 37104 38565 38565 37104 37104 38565 40026 37257 37104 37104"
## [17] "PMC13031693 PMC_DL/PMC13031693/supplementaryfiles/12672_2026_4726_MOESM2_ESM.xlsx Hsapiens 27 45909 45902 45722 45718 45717 45911 45907 45723 45910 45906 45724 45718 45908 45721 45904 45725 45901 45717 45903 45719 45905 45992 45720 45727 45914 45726 45912"
## [18] "PMC13030874 zip/viruses-4149909-supplementary.xlsx Hsapiens 24 42628 42432 42621 42705 42618 42431 42433 42436 42438 42617 42619 42430 42620 42623 42614 42627 42615 42622 42616 42624 42625 42435 42437 42434"
## [19] "PMC13030874 zip/viruses-4149909-supplementary.xlsx Hsapiens 2 42628 42432"
## [20] "PMC13030874 zip/viruses-4149909-supplementary.xlsx Hsapiens 2 42628 42432"
## [21] "PMC13025642 zip/Table_S4.xlsx Hsapiens 2 45915 45910"
## [22] "PMC13023209 PMC_DL/PMC13023209/supplementaryfiles/12888_2026_7918_MOESM3_ESM.xlsx Hsapiens 1 45723"
## [23] "PMC13023209 PMC_DL/PMC13023209/supplementaryfiles/12888_2026_7918_MOESM4_ESM.xlsx Hsapiens 1 45723"
## [24] "PMC13021997 PMC_DL/PMC13021997/supplementaryfiles/41398_2026_3897_MOESM2_ESM.xlsx Hsapiens 2 45536 45536"
## [25] "PMC13019979 PMC_DL/PMC13019979/supplementaryfiles/40246_2026_913_MOESM2_ESM.xlsx Hsapiens 58 37316 37316 37316 36951 36951 38596 36951 37316 37316 37500 37500 37500 38596 37500 37500 37500 37500 37500 37316 37316 38596 37316 37316 37316 37316 37316 37316 37316 36951 42248 40787 36951 36951 36951 36951 36951 39508 36951 37135 37135 37135 40238 38777 39508 39508 40787 40422 37316 40422 40603 36951 41153 41153 40422 40422 39508 41153 41153"
## [26] "PMC13019979 PMC_DL/PMC13019979/supplementaryfiles/40246_2026_913_MOESM2_ESM.xlsx Hsapiens 58 40422 40787 37316 37316 37316 37316 37316 37316 37316 37316 37135 37316 37316 39508 37316 40787 37135 37316 40422 37135 40422 37316 37316 36951 40238 37316 36951 39508 42248 36951 38777 40422 39508 38596 41153 36951 36951 36951 36951 41153 36951 36951 40603 39508 37500 36951 37500 38596 41153 38596 37500 37500 36951 41153 37500 37500 37500 37500"
## [27] "PMC13019979 PMC_DL/PMC13019979/supplementaryfiles/40246_2026_913_MOESM2_ESM.xlsx Hsapiens 58 40422 37500 36951 39508 37135 37316 38596 37316 40422 37500 36951 38777 39508 37135 37316 38596 42248 37316 40422 37500 36951 39508 41153 37135 40238 37316 37316 37316 36951 41153 37316 36951 37500 40787 36951 40603 37316 37500 36951 37316 37316 37500 36951 41153 37316 36951 37500 36951 39508 37316 37316 36951 40422 37500 40787 41153 37316 38596"
## [28] "PMC13018755 PMC_DL/PMC13018755/supplementaryfiles/gutjnl-75-3-s002.xlsx Hsapiens 1 37226"
## [29] "PMC13018755 PMC_DL/PMC13018755/supplementaryfiles/gutjnl-75-3-s002.xlsx Hsapiens 1 37226"
## [30] "PMC13014123 zip/Table_S2_Developmental_Transcriptomes_of_E._hainesii_20260202.xlsx Dmelanogaster 3 45721 45730 45730"
## [31] "PMC13016824 zip/Table_S4.xlsx Hsapiens 4 38961 40422 37500 40787"
## [32] "PMC13009199 PMC_DL/PMC13009199/supplementaryfiles/44276_2026_214_MOESM3_ESM.xlsx Ggallus 70 37469 37469 37834 37834 36892 36892 38200 38200 37104 37104 37104 37834 36892 36892 38200 38200 37469 37469 38200 38200 36892 36892 37104 37104 37834 37834 37469 37469 38200 38200 36892 37104 37469 37469 36892 37469 37104 37834 37834 37834 37834 37469 36892 38200 37104 37469 36892 38200 38200 37104 37834 37469 37469 36892 36892 37834 37834 37104 37104 38200 38200 38200 36892 36892 37469 37469 37104 37104 37834 37834"
## [33] "PMC13010944 PMC_DL/PMC13010944/supplementaryfiles/mmc5.xlsx Hsapiens 26 45992 45717 45726 45727 45718 45719 45720 45721 45722 45723 45724 45725 45915 45901 45910 45911 45912 45914 45902 45903 45904 45905 45906 45907 45908 45909"
## [34] "PMC13011747 PMC_DL/PMC13011747/supplementaryfiles/13059_2026_3992_MOESM2_ESM.xlsx Hsapiens 2 45722 45722"
## [35] "PMC13011747 PMC_DL/PMC13011747/supplementaryfiles/13059_2026_3992_MOESM2_ESM.xlsx Hsapiens 2 45722 45722"
## [36] "PMC13011774 PMC_DL/PMC13011774/supplementaryfiles/12870_2026_8336_MOESM1_ESM.xlsx Athaliana 15 45571 45568 45538 45384 45566 45567 45570 45537 45537 45572 45569 45383 45385 45536 45536"
## [37] "PMC13006575 PMC_DL/PMC13006575/supplementaryfiles/Table1.xls Hsapiens 1 44988"
## [38] "PMC13005615 zip/Figure_1/B-D/GSE9844.xlsx Hsapiens 26 45550 45544 45357 45546 45353 45353 45352 45356 45542 45545 45541 45543 45358 45547 45352 45359 45539 45362 45537 45360 45536 45538 45354 45361 45627 45355"
## [39] "PMC13005615 zip/Figure_1/B-D/GSE55547.xlsx Hsapiens 28 45536 45537 45354 45538 45353 45541 45546 45549 45545 45360 45361 45352 45357 45358 45627 45539 45355 45540 45362 45550 45543 45352 45356 45542 45547 45359 45353 45544"
## [40] "PMC13005615 zip/Figure_1/B-D/GSE55548.xlsx Hsapiens 28 45536 45537 45354 45538 45353 45546 45541 45627 45545 45355 45361 45549 45358 45539 45360 45357 45362 45547 45352 45352 45550 45544 45359 45540 45543 45542 45353 45356"
## [41] "PMC13004839 PMC_DL/PMC13004839/supplementaryfiles/41419_2026_8525_MOESM8_ESM.xlsx Mmusculus 27 37135 39326 39692 40422 38231 40603 37865 41153 38412 39508 37500 36951 39142 37681 41883 36951 42248 38777 38047 39873 38961 40787 40057 38596 37316 40238 37316"
## [42] "PMC13003602 PMC_DL/PMC13003602/supplementaryfiles/Table_4.XLSX Hsapiens 3 45720 45720 45720"
## [43] "PMC13004596 PMC_DL/PMC13004596/supplementaryfiles/elife-103167-supp6.xlsx Scerevisiae 1 45566"
## [44] "PMC13004596 PMC_DL/PMC13004596/supplementaryfiles/elife-103167-supp5.xlsx Hsapiens 11 44991 45171 45176 45183 45177 44987 45174 45180 44990 45179 45178"
## [45] "PMC13004595 PMC_DL/PMC13004595/supplementaryfiles/elife-108724-supp4.xlsx Mmusculus 27 44623 44627 44815 44814 44626 44807 44819 44628 44818 44631 44630 44811 44621 44624 44625 44622 44816 44629 44805 44621 44810 44622 44809 44808 44813 44806 44812"
## [46] "PMC13004595 PMC_DL/PMC13004595/supplementaryfiles/elife-108724-supp3.xlsx Rnorvegicus 3 44624 44624 44624"
## [47] "PMC13004595 PMC_DL/PMC13004595/supplementaryfiles/elife-108724-supp5.xlsx Mmusculus 1 44624"
## [48] "PMC13003292 PMC_DL/PMC13003292/supplementaryfiles/MEN-26-e70129-s001.xls Ggallus 1 2025/03/02"
## [49] "PMC13003292 PMC_DL/PMC13003292/supplementaryfiles/MEN-26-e70129-s001.xls Hsapiens 1 2025/03/02"
## [50] "PMC12999485 PMC_DL/PMC12999485/supplementaryfiles/41594_2026_1759_MOESM3_ESM.xlsx Hsapiens 29 45183 45177 44987 44986 44990 44986 44993 44992 45184 44988 44995 44994 44991 44987 44996 44989 45178 45170 45179 45176 45172 45181 45173 45174 45170 45171 45180 45175 45261"
## [51] "PMC12999485 PMC_DL/PMC12999485/supplementaryfiles/41594_2026_1759_MOESM6_ESM.xlsx Hsapiens 11 45353 45358 45360 45355 45352 45357 45359 45361 45354 45362 45356"
## [52] "PMC13001983 PMC_DL/PMC13001983/supplementaryfiles/pgen.1012030.s021.xlsx Hsapiens 1 45725"
## [53] "PMC13001983 PMC_DL/PMC13001983/supplementaryfiles/pgen.1012030.s034.xlsx Hsapiens 4 45725 45902 45912 45914"
## [54] "PMC13001983 PMC_DL/PMC13001983/supplementaryfiles/pgen.1012030.s057.xlsx Hsapiens 2 45902 45914"
## [55] "PMC13001983 PMC_DL/PMC13001983/supplementaryfiles/pgen.1012030.s056.xlsx Hsapiens 4 45902 45914 45725 45912"
## [56] "PMC13000003 PMC_DL/PMC13000003/supplementaryfiles/42003_2026_9628_MOESM4_ESM.xlsx Hsapiens 2 36951 37316"
## [57] "PMC13000244 PMC_DL/PMC13000244/supplementaryfiles/41467_2026_69269_MOESM3_ESM.xlsx Hsapiens 3 38412 40238 40238"
## [58] "PMC12999466 PMC_DL/PMC12999466/supplementaryfiles/41380_2025_3358_MOESM2_ESM.xlsx Hsapiens 27 45911 45901 45720 45721 45723 45719 45718 45725 45724 45908 45727 45903 45722 45718 45907 45905 45717 45904 45910 45717 45915 45726 45914 45909 45912 45992 45902"
## [59] "PMC12995690 PMC_DL/PMC12995690/supplementaryfiles/mmc3.xlsx Hsapiens 60 44986 44988 44993 44987 44988 44986 45176 45170 45175 45179 44992 44988 45176 45170 44986 45175 45180 44987 45178 45175 45170 44986 44988 45171 45170 45175 44986 44986 44987 45175 45178 44991 45170 44988 45170 45175 44986 44987 45180 45175 44986 44990 45171 45176 44987 45170 44988 44991 44990 45171 45175 45178 44992 44986 45176 45170 45175 45176 45178 44986"
## [60] "PMC12998166 PMC_DL/PMC12998166/supplementaryfiles/12883_2026_4725_MOESM1_ESM.xlsx Hsapiens 2 45721 45727"
## [61] "PMC12996886 zip/Table_S13.xlsx Hsapiens 2 44625 44807"
## [62] "PMC12996886 zip/Table_S13.xlsx Hsapiens 1 44809"
## [63] "PMC12996886 zip/Table_S13.xlsx Hsapiens 1 44807"
## [64] "PMC12996886 zip/Table_S13.xlsx Hsapiens 1 44815"
## [65] "PMC12996886 zip/Table_S14.xlsx Hsapiens 172 45261 44987 44992 45176 45174 45181 45175 45171 45176 45178 45173 45172 45179 45170 45177 45171 45171 45178 45173 45175 45174 45171 45176 45177 45180 45170 45172 45179 45172 45170 45174 45181 45175 45174 45171 45176 45178 45173 45172 45179 45177 45180 45176 45171 45178 45177 45173 45180 45171 45174 45176 45175 45179 45172 45173 44991 45170 45177 45180 45179 45172 45173 45178 45171 45183 45176 45174 45181 44991 45174 45173 44991 45170 45180 45179 45172 45173 45176 45171 45174 45175 45181 45179 45172 45173 45176 45175 45183 45176 45171 45174 45181 45175 45173 45178 45179 45170 45180 45177 45172 45177 45180 45170 45176 45183 45171 45175 45181 45174 45173 45178 45178 45173 45178 45183 45171 45175 45181 45174 45180 45177 45170 45179 45172 44991 45261 45180 45170 45172 45179 45173 45175 45181 45174 45176 45171 45178 45173 45181 45175 45176 45171 45180 45177 45170 45172 45179 45172 45179 45177 45180 45170 45175 45181 45174 45176 45183 45171 45178 45178 45176 45174 45181 45175 45176 45178 45173 45172 45179 45170 45180 45177"
## [66] "PMC12993451 zip/Supplementary_Table_S2.xlsx Hsapiens 1 45627"
## [67] "PMC12993451 zip/Supplementary_Table_S3.xlsx Hsapiens 1 45627"
## [68] "PMC12993451 zip/Supplementary_Table_S5.xlsx Hsapiens 1 45627"
## [69] "PMC12993451 zip/Supplementary_Table_S6.xlsx Hsapiens 1 45627"
## [70] "PMC12993451 zip/Supplementary_Table_S6.xlsx Hsapiens 1 45627"
## [71] "PMC12993451 zip/Supplementary_Table_S6.xlsx Hsapiens 1 45627"
## [72] "PMC12993451 zip/Supplementary_Table_S6.xlsx Hsapiens 1 45627"
## [73] "PMC12993451 zip/Supplementary_Table_S6.xlsx Hsapiens 1 45627"
## [74] "PMC12993451 zip/Supplementary_Table_S6.xlsx Hsapiens 1 45627"
## [75] "PMC12993451 zip/Supplementary_Table_S1.xlsx Hsapiens 1 45627"
## [76] "PMC12993451 zip/Supplementary_Table_S4.xlsx Hsapiens 1 45627"
## [77] "PMC12992800 PMC_DL/PMC12992800/supplementaryfiles/12672_2026_4635_MOESM1_ESM.xlsx Hsapiens 2 45717 45718"
## [78] "PMC12992800 PMC_DL/PMC12992800/supplementaryfiles/12672_2026_4635_MOESM1_ESM.xlsx Hsapiens 2 45717 45718"
## [79] "PMC12992822 PMC_DL/PMC12992822/supplementaryfiles/41467_2026_68966_MOESM3_ESM.xlsx Hsapiens 3 37104 37104 37104"
## [80] "PMC12991876 PMC_DL/PMC12991876/supplementaryfiles/NIHMS2144954-supplement-Supplementary_Table_3.xlsx Hsapiens 14 45175 44986 45172 45177 44993 44991 44989 45184 44995 45170 44992 45183 45171 45176"
## [81] "PMC12991876 PMC_DL/PMC12991876/supplementaryfiles/NIHMS2144954-supplement-Supplementary_Table_3.xlsx Hsapiens 13 44986 45184 44993 45176 44991 45172 45177 45170 45183 45179 44989 45180 45175"
## [82] "PMC12991876 PMC_DL/PMC12991876/supplementaryfiles/NIHMS2144954-supplement-Supplementary_Table_3.xlsx Hsapiens 11 45175 44986 45172 45177 44993 44991 44989 45184 45170 45183 45176"
## [83] "PMC12991876 PMC_DL/PMC12991876/supplementaryfiles/NIHMS2144954-supplement-Supplementary_Table_3.xlsx Hsapiens 8 45179 45172 45177 44996 44995 44991 44989 44993"
## [84] "PMC12991876 PMC_DL/PMC12991876/supplementaryfiles/NIHMS2144954-supplement-Supplementary_Table_3.xlsx Hsapiens 9 45172 44995 44986 45177 44987 45170 44987 44996 44988"
## [85] "PMC12991876 PMC_DL/PMC12991876/supplementaryfiles/NIHMS2144954-supplement-Supplementary_Table_1.xlsx Hsapiens 15 45180 44991 45178 45176 44991 44993 45179 45179 45171 45180 44992 45178 45175 44991 45179"
## [86] "PMC12991876 PMC_DL/PMC12991876/supplementaryfiles/NIHMS2144954-supplement-Supplementary_Table_1.xlsx Hsapiens 22 45175 45178 45176 44991 45180 45179 44992 44992 44992 44992 44992 45171 45171 44991 44991 45180 45179 45179 44988 45172 45180 44987"
## [87] "PMC12991876 PMC_DL/PMC12991876/supplementaryfiles/NIHMS2144954-supplement-Supplementary_Table_1.xlsx Hsapiens 14 45175 45178 45176 44991 45180 45179 44992 44992 44992 44992 44992 45171 45171 44991"
## [88] "PMC12987951 PMC_DL/PMC12987951/supplementaryfiles/41398_2026_3925_MOESM2_ESM.xlsx Hsapiens 4 40787 38961 39326 40057"
## [89] "PMC12988094 PMC_DL/PMC12988094/supplementaryfiles/10571_2026_1694_MOESM3_ESM.xlsx Mmusculus 1 43163"
## [90] "PMC12988094 PMC_DL/PMC12988094/supplementaryfiles/10571_2026_1694_MOESM3_ESM.xlsx Mmusculus 1 43352"
## [91] "PMC12988094 PMC_DL/PMC12988094/supplementaryfiles/10571_2026_1694_MOESM3_ESM.xlsx Mmusculus 2 43167 43348"
## [92] "PMC12988094 PMC_DL/PMC12988094/supplementaryfiles/10571_2026_1694_MOESM3_ESM.xlsx Mmusculus 1 43347"
## [93] "PMC12988094 PMC_DL/PMC12988094/supplementaryfiles/10571_2026_1694_MOESM3_ESM.xlsx Mmusculus 1 43344"
## [94] "PMC12987736 PMC_DL/PMC12987736/supplementaryfiles/41588_2026_2507_MOESM4_ESM.xlsx Hsapiens 2 37316 36951"
## [95] "PMC12984511 zip/Table_S3.xlsx Hsapiens 3 45906 45721 45717"
## [96] "PMC12985480 zip/ijms-4163223-supplementary.xlsx Hsapiens 27 37865 42248 37316 38596 38412 38777 40057 37681 38231 39692 39508 38961 39326 39873 37316 36951 40422 40787 39142 37135 37500 40603 36951 38047 41153 40238 41883"
## [97] "PMC12985480 zip/ijms-4163223-supplementary.xlsx Mmusculus 2 38108 37012"
## [98] "PMC12985480 zip/ijms-4163223-supplementary.xlsx Mmusculus 2 38108 37012"
## [99] "PMC12987650 PMC_DL/PMC12987650/supplementaryfiles/elife-89001-supp1.xlsx Hsapiens 7 44622 44621 44622 44622 44622 44622 44622"
## [100] "PMC12987650 PMC_DL/PMC12987650/supplementaryfiles/elife-89001-supp1.xlsx Hsapiens 7 45718 45717 45718 45718 45718 45718 45718"
## [101] "PMC12987650 PMC_DL/PMC12987650/supplementaryfiles/elife-89001-supp1.xlsx Hsapiens 207 44628 44625 44813 44622 44621 44626 44813 44624 44813 44809 44813 44811 44813 44818 44627 44896 44810 44813 44622 44622 44813 44807 44808 44623 44809 44808 44813 44623 44809 44813 44808 44808 44808 44623 44808 44809 44624 44815 44813 44808 44626 44810 44815 44621 44621 44625 44813 44629 44818 44813 44806 44625 44813 44815 44621 44624 44813 44626 44621 44621 44811 44811 44623 44622 44816 44622 44807 44813 44819 44622 44630 44623 44809 44811 44623 44621 44813 44625 44813 44810 44813 44621 44813 44813 44808 44812 44813 44623 44623 44818 44811 44622 44627 44622 44808 44630 44896 44813 44813 44626 44808 44623 44625 44622 44623 44808 44808 44809 44630 44813 44631 44814 44808 44812 44623 44810 44813 44806 44808 44815 44625 44813 44809 44621 44806 44809 44622 44807 44623 44809 44815 44813 44808 44626 44810 44815 44621 44621 44625 44813 44629 44818 44813 44628 44625 44628 44625 44625 44622 44813 44622 44815 44809 44623 44630 44813 44628 44631 44812 44625 44809 44621 44896 44623 44810 44814 44808 44812 44813 44810 44813 44809 44809 44808 44808 44626 44625 44808 44812 44812 44628 44621 44807 44625 44813 44815 44621 44624 44813 44626 44621 44621 44811 44811 44623 44622 44816 44622 44807 44813 44819 44622 44630 44623 44809 44811 44623"
## [102] "PMC12987650 PMC_DL/PMC12987650/supplementaryfiles/elife-89001-supp1.xlsx Hsapiens 207 45724 45721 45909 45718 45717 45722 45909 45720 45909 45905 45909 45907 45909 45914 45723 45992 45906 45909 45718 45718 45909 45903 45904 45719 45905 45904 45909 45719 45905 45909 45904 45904 45904 45719 45904 45905 45720 45911 45909 45904 45722 45906 45911 45717 45717 45721 45909 45725 45914 45909 45902 45721 45909 45911 45717 45720 45909 45722 45717 45717 45907 45907 45719 45718 45912 45718 45903 45909 45915 45718 45726 45719 45905 45907 45719 45717 45909 45721 45909 45906 45909 45717 45909 45909 45904 45908 45909 45719 45719 45914 45907 45718 45723 45718 45904 45726 45992 45909 45909 45722 45904 45719 45721 45718 45719 45904 45904 45905 45726 45909 45727 45910 45904 45908 45719 45906 45909 45902 45904 45911 45721 45909 45905 45717 45902 45905 45718 45903 45719 45905 45911 45909 45904 45722 45906 45911 45717 45717 45721 45909 45725 45914 45909 45724 45721 45724 45721 45721 45718 45909 45718 45911 45905 45719 45726 45909 45724 45727 45908 45721 45905 45717 45992 45719 45906 45910 45904 45908 45909 45906 45909 45905 45905 45904 45904 45722 45721 45904 45908 45908 45724 45717 45903 45721 45909 45911 45717 45720 45909 45722 45717 45717 45907 45907 45719 45718 45912 45718 45903 45909 45915 45718 45726 45719 45905 45907 45719"
## [103] "PMC12987650 PMC_DL/PMC12987650/supplementaryfiles/elife-89001-supp1.xlsx Hsapiens 14 45722 45909 45901 45721 45723 45910 45726 45907 45915 45727 45905 45725 45902 45912"
## [104] "PMC12987650 PMC_DL/PMC12987650/supplementaryfiles/elife-89001-supp1.xlsx Hsapiens 14 45721 45725 45912 45723 45902 45907 45910 45915 45726 45727 45722 45909 45905 45901"
## [105] "PMC12982611 PMC_DL/PMC12982611/supplementaryfiles/41467_2026_69152_MOESM4_ESM.xlsx Hsapiens 60 2025-03-06 2025-09-10 2025-09-02 2025-09-06 2025-09-07 2025-09-09 2025-09-06 2025-09-09 2025-03-06 2025-03-06 2025-09-02 2025-09-10 2025-09-02 2025-09-06 2025-09-07 2025-09-09 2025-09-09 2025-03-06 2025-09-15 2025-09-07 2025-09-10 2025-09-02 2025-09-06 2025-09-07 2025-09-08 2025-09-09 2025-09-10 2025-09-11 2025-09-02 2025-09-06 2025-09-07 2025-09-08 2025-09-09 2025-09-10 2025-09-02 2025-09-07 2025-09-09 2025-09-10 2025-09-11 2025-09-02 2025-09-06 2025-09-07 2025-09-08 2025-09-09 2025-09-10 2025-09-11 2025-09-02 2025-09-05 2025-09-06 2025-09-07 2025-09-08 2025-09-09 2025-09-10 2025-09-02 2025-09-07 2021-09-15 2021-09-15 2021-03-06 2021-09-15 2021-09-15"
## [106] "PMC12982611 PMC_DL/PMC12982611/supplementaryfiles/41467_2026_69152_MOESM8_ESM.xlsx Hsapiens 66 2025-09-09 2025-09-09 2025-09-06 2025-09-09 2025-09-09 2025-09-09 2025-09-09 2025-09-09 2025-09-07 2025-09-02 2025-09-09 2025-09-09 2025-09-09 2025-09-09 2025-09-07 2025-09-07 2025-09-07 2025-09-06 2025-09-07 2025-09-09 2025-09-02 2025-09-02 2025-09-06 2025-09-09 2025-09-09 2025-09-09 2025-09-06 2025-09-09 2025-09-09 2025-09-09 2025-09-02 2025-09-07 2025-09-06 2025-09-06 2025-09-06 2025-09-09 2025-09-09 2025-09-09 2025-09-09 2025-09-06 2025-09-06 2025-09-09 2025-09-02 2025-09-09 2025-09-06 2025-09-09 2025-09-07 2025-09-02 2025-09-02 2025-09-09 2025-09-07 2025-09-09 2025-09-02 2025-09-09 2025-09-07 2025-09-02 2025-09-09 2025-09-09 2025-09-02 2025-09-07 2025-09-09 2025-09-09 2025-09-09 2025-09-09 2025-09-06 2025-09-09"
## [107] "PMC12982611 PMC_DL/PMC12982611/supplementaryfiles/41467_2026_69152_MOESM15_ESM.xlsx Hsapiens 60 45722 45910 45902 45906 45907 45909 45906 45909 45722 45722 45902 45910 45902 45906 45907 45909 45909 45722 45915 45907 45910 45902 45906 45907 45908 45909 45910 45911 45902 45906 45907 45908 45909 45910 45902 45907 45909 45910 45911 45902 45906 45907 45908 45909 45910 45911 45902 45905 45906 45907 45908 45909 45910 45902 45907 44454 44454 44261 44454 44454"
## [108] "PMC12985386 PMC_DL/PMC12985386/supplementaryfiles/mmc5.xlsx Hsapiens 6 45903 45909 45910 45718 45717 45910"
## [109] "PMC12985386 PMC_DL/PMC12985386/supplementaryfiles/mmc2.xlsx Hsapiens 24 45546 45352 45352 45352 45542 45544 45542 45358 45536 45542 45544 45541 45353 45545 45361 45357 45542 45546 45545 45542 45542 45545 45537 45537"
## [110] "PMC12987568 zip/TableS1.xlsx Hsapiens 140 45723 45908 45727 45910 45901 45720 45904 45906 45912 45914 45901 45903 45718 45725 45717 45718 45914 45718 45905 45723 45717 45723 45904 45901 45914 45915 45722 45717 45902 45718 45725 45724 45910 45720 45903 45904 45727 45907 45912 45720 45992 45723 45992 45717 45907 45718 45724 45723 45912 45907 45724 45910 45905 45904 45717 45718 45717 45915 45904 45722 45914 45911 45726 45914 45909 45721 45912 45719 45915 45720 45718 45905 45992 45912 45717 45719 45909 45906 45725 45721 45915 45909 45721 45902 45906 45718 45727 45720 45722 45907 45992 45908 45722 45721 45911 45721 45718 45909 45726 45717 45908 45724 45722 45717 45909 45992 45718 45911 45906 45903 45911 45726 45726 45719 45903 45902 45908 45908 45911 45915 45903 45724 45725 45727 45901 45910 45719 45725 45902 45907 45719 45717 45726 45727 45902 45905 45905 45906 45910 45901"
## [111] "PMC12979158 PMC_DL/PMC12979158/supplementaryfiles/Table2.xlsx Hsapiens 1 46084"
## [112] "PMC12979158 PMC_DL/PMC12979158/supplementaryfiles/Table3.xlsx Hsapiens 1 46084"
## [113] "PMC12979829 PMC_DL/PMC12979829/supplementaryfiles/41467_2026_69561_MOESM3_ESM.xlsx Hsapiens 3 37500 40787 40057"
## [114] "PMC12978397 PMC_DL/PMC12978397/supplementaryfiles/wjon-17-02-247-s004.xlsx Hsapiens 2 45904 45718"
## [115] "PMC12978397 PMC_DL/PMC12978397/supplementaryfiles/wjon-17-02-247-s002.xlsx Hsapiens 1 45717"
## [116] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp2.xlsx Mmusculus 1 2023-03-05"
## [117] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp2.xlsx Mmusculus 4 2023-09-07 2023-03-05 2023-03-01 2023-09-04"
## [118] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp2.xlsx Mmusculus 1 2023-03-01"
## [119] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp2.xlsx Mmusculus 7 2023-03-01 2023-03-01 2023-03-02 2023-03-05 2023-03-06 2023-09-11 2023-09-08"
## [120] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp2.xlsx Mmusculus 23 2023-09-08 2023-09-07 2023-03-01 2023-09-11 2023-09-04 2023-03-01 2023-03-06 2023-09-11 2023-03-02 2023-03-05 2023-03-01 2023-09-11 2023-03-07 2023-03-05 2023-03-02 2023-09-07 2023-09-09 2023-09-04 2023-03-01 2023-09-10 2023-03-10 2023-09-04 2023-03-01"
## [121] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp2.xlsx Mmusculus 1 2023-03-02"
## [122] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp3.xlsx Mmusculus 24 2023-03-04 2023-09-02 2023-03-01 2023-03-02 2023-03-07 2023-09-06 2023-09-11 2023-03-08 2023-09-01 2023-09-10 2023-03-09 2023-03-01 2023-09-07 2023-09-08 2023-09-04 2023-03-10 2023-09-09 2023-03-11 2023-03-06 2023-09-03 2023-09-05 2023-03-02 2023-03-03 2023-03-05"
## [123] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp1.xlsx Mmusculus 11 2023-09-07 2023-09-09 2023-09-01 2023-03-01 2023-09-11 2023-03-02 2023-09-07 2023-03-05 2023-09-09 2023-09-01 2023-09-06"
## [124] "PMC12978698 PMC_DL/PMC12978698/supplementaryfiles/elife-100832-supp1.xlsx Mmusculus 73 2023-03-07 2023-09-01 2023-09-09 2023-09-02 2023-03-01 2023-03-02 2023-03-07 2023-09-11 2023-09-10 2023-09-07 2023-09-08 2023-09-04 2023-03-10 2023-09-09 2023-09-05 2023-03-02 2023-03-03 2023-03-05 2023-03-01 2023-03-07 2023-09-11 2023-03-08 2023-03-10 2023-03-02 2023-03-03 2023-03-05 2023-03-01 2023-03-07 2023-03-08 2023-09-07 2023-03-03 2023-03-05 2023-09-02 2023-03-01 2023-03-02 2023-03-07 2023-09-06 2023-09-11 2023-03-08 2023-09-01 2023-09-10 2023-03-09 2023-09-07 2023-09-08 2023-09-04 2023-09-09 2023-03-06 2023-09-03 2023-09-05 2023-03-02 2023-03-03 2023-03-05 2023-03-07 2023-09-11 2023-09-10 2023-09-07 2023-09-08 2023-09-04 2023-09-09 2023-03-06 2023-09-03 2023-03-03 2023-09-02 2023-03-07 2023-03-08 2023-03-01 2023-09-07 2023-09-08 2023-09-04 2023-09-09 2023-03-06 2023-03-02 2023-03-03"
## [125] "PMC12978544 zip/TabS14_GOSupplementaryTable.xlsx Dmelanogaster 3 45170 45171 45173"
## [126] "PMC12977612 PMC_DL/PMC12977612/supplementaryfiles/12864_2026_12618_MOESM5_ESM.xlsx Ggallus 2 38596 38596"
## [127] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 23 45718 45903 45904 45718 45907 45906 45723 45911 45725 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45727 45909 45910 45721"
## [128] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 28 45718 45903 45904 45718 45907 45906 45723 45911 45725 45912 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45901 45915 45727 45909 45717 45910 45721 45901"
## [129] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 5 37104 37469 37834 38200 36892"
## [130] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 1 36892"
## [131] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 23 45718 45903 45904 45718 45907 45906 45723 45911 45725 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45727 45909 45910 45721"
## [132] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 28 45718 45903 45904 45718 45907 45906 45723 45911 45725 45912 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45901 45915 45727 45909 45717 45910 45721 45901"
## [133] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 7 45907 45722 45914 45911 45727 45724 45909"
## [134] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 23 45718 45903 45904 45718 45907 45906 45723 45911 45725 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45727 45909 45910 45721"
## [135] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 28 45718 45903 45904 45718 45907 45906 45723 45911 45725 45912 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45901 45915 45727 45909 45717 45910 45721 45901"
## [136] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 7 45907 45722 45914 45911 45727 45724 45909"
## [137] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 23 45718 45903 45904 45718 45907 45906 45723 45911 45725 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45727 45909 45910 45721"
## [138] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 28 45718 45903 45904 45718 45907 45906 45723 45911 45725 45912 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45901 45915 45727 45909 45717 45910 45721 45901"
## [139] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 7 45907 45722 45914 45911 45727 45724 45909"
## [140] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 23 45718 45903 45904 45718 45907 45906 45723 45911 45725 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45727 45909 45910 45721"
## [141] "PMC12975130 PMC_DL/PMC12975130/supplementaryfiles/elife-106846-supp2.xlsx Hsapiens 28 45718 45903 45904 45718 45907 45906 45723 45911 45725 45912 45720 45717 45722 45914 45908 45724 45902 45992 45726 45719 45901 45915 45727 45909 45717 45910 45721 45901"
## [142] "PMC12974471 PMC_DL/PMC12974471/supplementaryfiles/pnas.2525865123.sd01.xlsx Hsapiens 2 43901 43891"
## [143] "PMC12971484 PMC_DL/PMC12971484/supplementaryfiles/41593_2025_2154_MOESM8_ESM.xlsx Hsapiens 1 37316"
## [144] "PMC12971484 PMC_DL/PMC12971484/supplementaryfiles/41593_2025_2154_MOESM5_ESM.xlsx Hsapiens 2 37316 37316"
## [145] "PMC12971484 PMC_DL/PMC12971484/supplementaryfiles/41593_2025_2154_MOESM5_ESM.xlsx Hsapiens 271 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316"
## [146] "PMC12971484 PMC_DL/PMC12971484/supplementaryfiles/41593_2025_2154_MOESM13_ESM.xlsx Hsapiens 5 45720 45725 45718 45718 45721"
## [147] "PMC12971484 PMC_DL/PMC12971484/supplementaryfiles/41593_2025_2154_MOESM11_ESM.xlsx Hsapiens 242 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 39508 39508 39508 39508 39508 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 38412 39873 39873 39873 39873 39873 39873 39873 39873 39873 39873 39873 39873 39873 39873 39873 39873 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38047 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777 38777"
## [148] "PMC12968393 zip/LvMaherSuppData.xlsx Mmusculus 26 45352 45353 45352 45361 45362 45353 45354 45355 45356 45357 45358 45359 45360 45536 45545 45546 45547 45549 45537 45538 45539 45540 45541 45542 45543 45544"
## [149] "PMC12968393 zip/LvMaherSuppData.xlsx Mmusculus 26 45717 45718 45717 45726 45727 45718 45719 45720 45721 45722 45723 45724 45725 45901 45910 45911 45912 45914 45902 45903 45904 45905 45906 45907 45908 45909"
## [150] "PMC12968393 zip/LvMaherSuppData.xlsx Mmusculus 19 45725 45910 45909 45909 45908 45717 45718 45904 45722 45903 45903 45912 45718 45719 45723 45914 45911 45724 45907"
## [151] "PMC12965172 PMC_DL/PMC12965172/supplementaryfiles/peerj-14-20885-s004.xlsx Hsapiens 3 45360 45359 45536"
## [152] "PMC12964230 zip/Supplementary_tables.xlsx Hsapiens 26 45721 45904 45915 45718 45717 45909 45912 45723 45719 45910 45726 45907 45724 45727 45906 45718 45717 45903 45901 45992 45725 45911 45902 45720 45722 45908"
## [153] "PMC12964230 zip/Supplementary_tables.xlsx Hsapiens 26 45717 45906 45911 45718 45718 45912 45909 45908 45915 45721 45726 45723 45910 45727 45901 45725 45719 45902 45722 45903 45724 45992 45904 45717 45907 45720"
## [154] "PMC12964230 zip/Supplementary_tables.xlsx Hsapiens 26 45717 45906 45718 45904 45911 45908 45717 45725 45901 45726 45903 45727 45902 45722 45721 45907 45719 45718 45910 45912 45724 45992 45909 45720 45723 45915"
## [155] "PMC12964230 zip/Supplementary_tables.xlsx Hsapiens 5 45904 45907 45901 45906 45909"
## [156] "PMC12964230 zip/Supplementary_tables.xlsx Hsapiens 5 45904 45907 45901 45906 45909"
## [157] "PMC12965291 zip/aec7817_data_s1.xlsx Athaliana 4 37865 37165 37135 38626"
## [158] "PMC12965291 zip/aec7817_data_s1.xlsx Athaliana 1 37865"
## [159] "PMC12965291 zip/aec7817_data_s1.xlsx Athaliana 3 37865 36982 37135"
## [160] "PMC12963367 PMC_DL/PMC12963367/supplementaryfiles/41467_2026_68934_MOESM9_ESM.xlsx Hsapiens 2 45914 45914"
## [161] "PMC12963367 PMC_DL/PMC12963367/supplementaryfiles/41467_2026_68934_MOESM9_ESM.xlsx Hsapiens 86 45724 45904 45909 45724 45907 45903 45911 45909 45909 45910 45909 45910 45911 45911 45909 45911 45906 45909 45910 45723 45723 45911 45911 45911 45911 45911 45724 45724 45904 45904 45909 45911 45910 45901 45717 45717 45724 45724 45723 45723 45904 45904 45909 45904 45904 45909 45904 45909 45909 45911 45907 45909 45909 45906 45909 45909 45903 45909 45724 45902 45910 45724 45724 45910 45910 45724 45724 45902 45723 45909 45724 45902 45723 45722 45724 45724 45724 45910 45724 45724 45724 45910 45724 45910 45724 45910"
## [162] "PMC12962868 PMC_DL/PMC12962868/supplementaryfiles/NIHMS2145465-supplement-Supplementary_Table_6.xlsx Mmusculus 25 44987 44986 44995 44996 44987 44988 44989 44990 44991 44992 44993 44994 45184 45170 45179 45180 45183 45171 45172 45173 45174 45175 45176 45177 45178"
## [163] "PMC12962868 PMC_DL/PMC12962868/supplementaryfiles/NIHMS2145465-supplement-Supplementary_Table_6.xlsx Mmusculus 26 44986 44987 44986 44995 44996 44987 44988 44989 44990 44991 44992 44993 44994 45184 45170 45179 45180 45183 45171 45172 45173 45174 45175 45176 45177 45178"
## [164] "PMC12962868 PMC_DL/PMC12962868/supplementaryfiles/NIHMS2145465-supplement-Supplementary_Table_6.xlsx Mmusculus 24 44987 44986 44995 44996 44987 44988 44989 44990 44991 44992 44993 44994 45184 45170 45179 45180 45171 45172 45173 45174 45175 45176 45177 45178"
## [165] "PMC12962868 PMC_DL/PMC12962868/supplementaryfiles/NIHMS2145465-supplement-Supplementary_Table_6.xlsx Mmusculus 26 44986 44987 44986 44995 44996 44987 44988 44989 44990 44991 44992 44993 44994 45184 45170 45179 45180 45181 45171 45172 45173 45174 45175 45176 45177 45178"
## [166] "PMC12961773 PMC_DL/PMC12961773/supplementaryfiles/12931_2026_3565_MOESM1_ESM.xlsx Hsapiens 4 45172 45172 45180 45183"
## [167] "PMC12960846 PMC_DL/PMC12960846/supplementaryfiles/41598_2026_39101_MOESM2_ESM.xlsx Mmusculus 12 44987 45184 44993 44988 44990 44995 44996 44994 44989 44992 44991 44986"
## [168] "PMC12960846 PMC_DL/PMC12960846/supplementaryfiles/41598_2026_39101_MOESM2_ESM.xlsx Mmusculus 12 45184 44987 44993 44986 44991 44988 44989 44994 44996 44992 44995 44990"
## [169] "PMC12960846 PMC_DL/PMC12960846/supplementaryfiles/41598_2026_39101_MOESM2_ESM.xlsx Mmusculus 12 45184 44993 44991 44986 44987 44989 44996 44992 44988 44995 44994 44990"
## [170] "PMC12960846 PMC_DL/PMC12960846/supplementaryfiles/41598_2026_39101_MOESM3_ESM.xlsx Mmusculus 12 44987 45184 44993 44988 44990 44995 44996 44994 44989 44992 44991 44986"
## [171] "PMC12960846 PMC_DL/PMC12960846/supplementaryfiles/41598_2026_39101_MOESM3_ESM.xlsx Mmusculus 12 45184 44987 44993 44986 44991 44988 44989 44994 44996 44992 44995 44990"
## [172] "PMC12960846 PMC_DL/PMC12960846/supplementaryfiles/41598_2026_39101_MOESM3_ESM.xlsx Mmusculus 12 45184 44993 44991 44986 44987 44989 44996 44992 44988 44995 44994 44990"
## [173] "PMC12960819 PMC_DL/PMC12960819/supplementaryfiles/41598_2026_39325_MOESM2_ESM.xls Hsapiens 13 2026/12/01 2026/03/01 2026/03/10 2026/03/11 2026/03/02 2026/03/03 2026/03/04 2026/03/05 2026/03/06 2026/03/07 2026/03/08 2026/03/09 2026/09/15"
## [174] "PMC12960819 PMC_DL/PMC12960819/supplementaryfiles/41598_2026_39325_MOESM2_ESM.xls Hsapiens 9 2026/12/01 2026/03/01 2026/03/02 2026/03/03 2026/03/05 2026/03/06 2026/03/07 2026/03/08 2026/09/15"
## [175] "PMC12960819 PMC_DL/PMC12960819/supplementaryfiles/41598_2026_39325_MOESM2_ESM.xls Hsapiens 9 2026/12/01 2026/03/01 2026/03/02 2026/03/03 2026/03/05 2026/03/06 2026/03/07 2026/03/08 2026/09/15"
## [176] "PMC12960819 PMC_DL/PMC12960819/supplementaryfiles/41598_2026_39325_MOESM2_ESM.xls Hsapiens 9 2026/12/01 2026/03/01 2026/03/02 2026/03/03 2026/03/05 2026/03/06 2026/03/07 2026/03/08 2026/09/15"
## [177] "PMC12959415 zip/adz4758_tables_s1_to_s35.xlsx Hsapiens 1 45992"
## [178] "PMC12959415 zip/adz4758_tables_s1_to_s35.xlsx Mmusculus 19 45717 45719 45727 45719 45717 45720 45727 45717 45719 45717 45719 45727 45717 45720 45719 45717 45727 45724 45717"
## [179] "PMC12957397 PMC_DL/PMC12957397/supplementaryfiles/41598_2026_36534_MOESM6_ESM.xlsx Hsapiens 1 44994"
## [180] "PMC12957397 PMC_DL/PMC12957397/supplementaryfiles/41598_2026_36534_MOESM6_ESM.xlsx Hsapiens 3 44992 45261 44995"
## [181] "PMC12957397 PMC_DL/PMC12957397/supplementaryfiles/41598_2026_36534_MOESM5_ESM.xlsx Hsapiens 11 44994 44989 44991 44988 44996 44993 44990 45184 45261 44992 44995"
## [182] "PMC12957397 PMC_DL/PMC12957397/supplementaryfiles/41598_2026_36534_MOESM5_ESM.xlsx Hsapiens 11 44995 44992 45184 45261 44990 44993 44989 44996 44988 44991 44994"
## [183] "PMC12957397 PMC_DL/PMC12957397/supplementaryfiles/41598_2026_36534_MOESM4_ESM.xlsx Hsapiens 33 45184 44989 44988 44992 44994 44994 44993 44993 44994 45184 45261 45184 44990 44989 44992 44991 44995 44990 44993 45261 44996 44996 44995 44996 44995 44989 44992 44991 44990 45261 44988 44991 44988"
## [184] "PMC12957838 PMC_DL/PMC12957838/supplementaryfiles/mmc4.xlsx Hsapiens 23 45172 44990 45171 45184 45183 44993 45180 44991 44988 44994 45176 45170 45173 45177 44989 44995 44996 45174 45175 44992 45179 45178 45181"
## [185] "PMC12957787 PMC_DL/PMC12957787/supplementaryfiles/mmc2.xlsx Hsapiens 6 45726 45718 45724 45901 45901 45726"
## [186] "PMC11897779 PMC_DL/PMC11897779/supplementaryfiles/mmc2.xlsx Hsapiens 1 45355"
## [187] "PMC12953882 PMC_DL/PMC12953882/supplementaryfiles/41598_2026_38052_MOESM2_ESM.xlsx Hsapiens 14 40057 39326 39326 39326 39326 39326 38231 38231 38961 38961 39326 37500 37500 37500"
## [188] "PMC12953642 PMC_DL/PMC12953642/supplementaryfiles/41467_2026_68608_MOESM4_ESM.xlsx Hsapiens 2 45543 45360"
## [189] "PMC12956043 PMC_DL/PMC12956043/supplementaryfiles/MMI-125-185-s002.xlsx Hsapiens 1 37012"
## [190] "PMC12956043 PMC_DL/PMC12956043/supplementaryfiles/MMI-125-185-s002.xlsx Hsapiens 1 37012"
## [191] "PMC12956043 PMC_DL/PMC12956043/supplementaryfiles/MMI-125-185-s002.xlsx Hsapiens 1 37012"
## [192] "PMC12956043 PMC_DL/PMC12956043/supplementaryfiles/MMI-125-185-s002.xlsx Hsapiens 1 37012"
## [193] "PMC12956043 PMC_DL/PMC12956043/supplementaryfiles/MMI-125-185-s002.xlsx Hsapiens 1 37012"
## [194] "PMC12956043 PMC_DL/PMC12956043/supplementaryfiles/MMI-125-185-s002.xlsx Hsapiens 1 37012"
## [195] "PMC12953866 PMC_DL/PMC12953866/supplementaryfiles/44320_2025_173_MOESM7_ESM.xlsx Hsapiens 6 45721 45721 45721 45721 45721 45721"
## [196] "PMC12953866 PMC_DL/PMC12953866/supplementaryfiles/44320_2025_173_MOESM9_ESM.xlsx Hsapiens 2 45721 45721"
## [197] "PMC12953866 zip/MSB-2025-13191_SourceDataForFigure_EV/Figure_EV1/EV1A/gene-to-microbiome_MR_pairs.xlsx Hsapiens 6 45721 45721 45721 45721 45721 45721"
## [198] "PMC12953866 zip/MSB-2025-13191_SourceDataForFigure_EV/Figure_EV1/EV1C-D/gene-to-microbiome_MR_pairs.xlsx Hsapiens 6 45721 45721 45721 45721 45721 45721"
## [199] "PMC12953866 zip/MSB-2025-13191_SourceDataForFigure_EV/Figure_EV1/EV1F/microbiome-to-gene_expression_MR_results.xlsx Hsapiens 2 45721 45721"
## [200] "PMC12953866 zip/MSB-2025-13191_SourceDataForFigure_EV/Figure_EV2/EV2A-D/gene-to-microbiome_MR_pairs.xlsx Hsapiens 6 45721 45721 45721 45721 45721 45721"
## [201] "PMC12953866 zip/MSB-2025-13191_SourceDataForFigure_2/2A-C/gene-to-microbiome_MR_pairs.xlsx Hsapiens 6 45721 45721 45721 45721 45721 45721"
## [202] "PMC12953866 zip/MSB-2025-13191_SourceDataForFigure_1/1C-F/gene-to-microbiome_MR_pairs.xlsx Hsapiens 6 45721 45721 45721 45721 45721 45721"
## [203] "PMC12952131 PMC_DL/PMC12952131/supplementaryfiles/12957_2026_4234_MOESM3_ESM.xlsx Hsapiens 26 45550 45545 45358 45537 45352 45354 45542 45356 45544 45546 45627 45353 45355 45549 45357 45543 45361 45359 45547 45538 45536 45362 45541 45360 45539 45540"
## [204] "PMC12951959 zip/Supplemental_Tables/Supplemental_Table_S11.xlsx Mmusculus 11 45718 45722 45723 45722 45724 45723 45724 45722 45722 45724 45723"
## [205] "PMC12948414 PMC_DL/PMC12948414/supplementaryfiles/jci-136-195652-s021.xlsx Hsapiens 33 45362 45539 45353 45540 45538 45361 45546 45352 45543 45544 45359 45356 45547 45541 45360 45352 45549 45358 45536 45353 45536 45357 45353 45627 45550 45539 45352 45540 45537 45355 45545 45542 45354"
## [206] "PMC12948414 PMC_DL/PMC12948414/supplementaryfiles/jci-136-195652-s021.xlsx Hsapiens 33 45362 45539 45353 45540 45538 45361 45546 45352 45543 45544 45359 45356 45547 45541 45360 45352 45549 45358 45536 45353 45536 45357 45353 45627 45550 45539 45352 45540 45537 45355 45545 45542 45354"
## [207] "PMC12948831 PMC_DL/PMC12948831/supplementaryfiles/421_2025_5987_MOESM3_ESM.xlsx Hsapiens 8 37316 36951 36951 37316 36951 37316 36951 37316"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
## 5 2 1 3 158
## Mmusculus Rnorvegicus Scerevisiae
## 36 1 1par(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##
## PMC10060313 PMC11850471 PMC11897779 PMC12698805 PMC12891060 PMC12948414
## 1 2 1 6 1 2
## PMC12948831 PMC12951959 PMC12952131 PMC12953642 PMC12953866 PMC12953882
## 1 1 1 1 8 1
## PMC12956043 PMC12957397 PMC12957787 PMC12957838 PMC12959415 PMC12960819
## 6 5 1 1 2 4
## PMC12960846 PMC12961773 PMC12962868 PMC12963367 PMC12964230 PMC12965172
## 6 1 4 2 5 1
## PMC12965291 PMC12968393 PMC12971484 PMC12974471 PMC12975130 PMC12977612
## 3 3 5 1 15 1
## PMC12978397 PMC12978544 PMC12978698 PMC12979158 PMC12979829 PMC12982611
## 2 1 9 2 1 3
## PMC12984511 PMC12985386 PMC12985480 PMC12987568 PMC12987650 PMC12987736
## 1 2 3 1 6 1
## PMC12987951 PMC12988094 PMC12991876 PMC12992800 PMC12992822 PMC12993451
## 1 5 8 2 1 11
## PMC12995690 PMC12996886 PMC12998166 PMC12999466 PMC12999485 PMC13000003
## 1 5 1 1 2 1
## PMC13000244 PMC13001983 PMC13003292 PMC13003602 PMC13004595 PMC13004596
## 1 4 2 1 3 2
## PMC13004839 PMC13005615 PMC13006575 PMC13009199 PMC13010944 PMC13011747
## 1 3 1 1 1 2
## PMC13011774 PMC13014123 PMC13016824 PMC13018755 PMC13019979 PMC13021997
## 1 1 1 2 3 1
## PMC13023209 PMC13025642 PMC13030874 PMC13031693 PMC13032165 PMC13034595
## 2 1 3 1 1 3
## PMC13034653 PMC13035081
## 1 1summary(as.numeric(DIST))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.000 1.000 1.500 2.587 3.000 15.000hist(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
## 29 PMC12975130 15
## 48 PMC12993451 11
## 33 PMC12978698 9
## 11 PMC12953866 8
## 45 PMC12991876 8
## 4 PMC12698805 6
## 13 PMC12956043 6
## 19 PMC12960846 6
## 41 PMC12987650 6
## 14 PMC12957397 5
## 23 PMC12964230 5
## 27 PMC12971484 5
## 44 PMC12988094 5
## 50 PMC12996886 5
## 18 PMC12960819 4
## 21 PMC12962868 4
## 56 PMC13001983 4
## 25 PMC12965291 3
## 26 PMC12968393 3
## 36 PMC12982611 3MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES## [1] "PMC12975130"# 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## PMC10060313 PMC11850471 PMC11897779 PMC12698805 PMC12891060 PMC12948414
## 6 7 1 230 3 66
## PMC12948831 PMC12951959 PMC12952131 PMC12953642 PMC12953866 PMC12953882
## 8 11 26 2 40 14
## PMC12956043 PMC12957397 PMC12957787 PMC12957838 PMC12959415 PMC12960819
## 6 59 6 23 20 40
## PMC12960846 PMC12961773 PMC12962868 PMC12963367 PMC12964230 PMC12965172
## 72 4 101 88 88 3
## PMC12965291 PMC12968393 PMC12971484 PMC12974471 PMC12975130 PMC12977612
## 8 71 521 2 282 2
## PMC12978397 PMC12978544 PMC12978698 PMC12979158 PMC12979829 PMC12982611
## 3 3 145 2 3 186
## PMC12984511 PMC12985386 PMC12985480 PMC12987568 PMC12987650 PMC12987736
## 3 30 31 140 456 2
## PMC12987951 PMC12988094 PMC12991876 PMC12992800 PMC12992822 PMC12993451
## 4 6 106 4 3 11
## PMC12995690 PMC12996886 PMC12998166 PMC12999466 PMC12999485 PMC13000003
## 60 177 2 27 40 2
## PMC13000244 PMC13001983 PMC13003292 PMC13003602 PMC13004595 PMC13004596
## 3 11 2 3 31 12
## PMC13004839 PMC13005615 PMC13006575 PMC13009199 PMC13010944 PMC13011747
## 27 82 1 70 26 4
## PMC13011774 PMC13014123 PMC13016824 PMC13018755 PMC13019979 PMC13021997
## 15 3 4 2 174 2
## PMC13023209 PMC13025642 PMC13030874 PMC13031693 PMC13032165 PMC13034595
## 2 2 28 27 16 4
## PMC13034653 PMC13035081
## 26 1hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
head(NERR_DF,20)## NERR
## PMC12971484 521
## PMC12987650 456
## PMC12975130 282
## PMC12698805 230
## PMC12982611 186
## PMC12996886 177
## PMC13019979 174
## PMC12978698 145
## PMC12987568 140
## PMC12991876 106
## PMC12962868 101
## PMC12963367 88
## PMC12964230 88
## PMC13005615 82
## PMC12960846 72
## PMC12968393 71
## PMC13009199 70
## PMC12948414 66
## PMC12995690 60
## PMC12957397 59MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR## [1] "PMC12971484"Journals affected
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
### JSON PARSING is more reliable than XML
ARTICLES <- esummary( GENELIST_ERROR_ARTICLES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA$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] 58par(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] "12975130"
##
## $result$`12975130`
## $result$`12975130`$uid
## [1] "12975130"
##
## $result$`12975130`$pubdate
## [1] "2026 Mar 10"
##
## $result$`12975130`$epubdate
## [1] "2026 Mar 10"
##
## $result$`12975130`$printpubdate
## [1] ""
##
## $result$`12975130`$source
## [1] "Elife"
##
## $result$`12975130`$authors
## name authtype
## 1 Monziani A Author
## 2 Unfried JP Author
## 3 Cvetanovic T Author
## 4 Ulitsky I Author
##
## $result$`12975130`$title
## [1] "EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology."
##
## $result$`12975130`$volume
## [1] "14"
##
## $result$`12975130`$issue
## [1] ""
##
## $result$`12975130`$pages
## [1] ""
##
## $result$`12975130`$articleids
## idtype value
## 1 pmid 41805684
## 2 pmcid PMC12975130
## 3 doi 10.7554/eLife.106846
## 4 pii 106846
##
## $result$`12975130`$fulljournalname
## [1] "eLife"
##
## $result$`12975130`$sortdate
## [1] "2026/03/10 00:00"
##
## $result$`12975130`$pmclivedate
## [1] "2026/03/11"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] "12971484"
##
## $result$`12971484`
## $result$`12971484`$uid
## [1] "12971484"
##
## $result$`12971484`$pubdate
## [1] "2026 Mar"
##
## $result$`12971484`$epubdate
## [1] "2025 Dec 18"
##
## $result$`12971484`$printpubdate
## [1] "2026 Mar"
##
## $result$`12971484`$source
## [1] "Nat Neurosci"
##
## $result$`12971484`$authors
## name authtype
## 1 Green NFO Author
## 2 Sutton GJ Author
## 3 Pérez-Burillo J Author
## 4 Wang J Author
## 5 Bagot S Author
## 6 Danon HG Author
## 7 Walsh K Author
## 8 Gokool A Author
## 9 Miles SA Author
## 10 Yang G Author
## 11 Herring CA Author
## 12 Liang Y Author
## 13 Pfundstein G Author
## 14 Sytnyk V Author
## 15 Alinejad-Rokny H Author
## 16 Lister R Author
## 17 Rosenbluh J Author
## 18 Gagnon-Bartsch JA Author
## 19 Voineagu I Author
##
## $result$`12971484`$title
## [1] "CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease."
##
## $result$`12971484`$volume
## [1] "29"
##
## $result$`12971484`$issue
## [1] "3"
##
## $result$`12971484`$pages
## [1] "703-716"
##
## $result$`12971484`$articleids
## idtype value
## 1 pmid 41413662
## 2 pmcid PMC12971484
## 3 doi 10.1038/s41593-025-02154-3
## 4 pii 10.1038/s41593-025-02154-3
##
## $result$`12971484`$fulljournalname
## [1] "Nature neuroscience"
##
## $result$`12971484`$sortdate
## [1] "2026/03/01 00:00"
##
## $result$`12971484`$pmclivedate
## [1] "2026/03/11"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 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## 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
##
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] readxl_1.5.0 reutils_0.2.3 xml2_1.5.2 jsonlite_2.0.0
##
## loaded via a namespace (and not attached):
## [1] assertthat_0.2.1 digest_0.6.39 XML_3.99-0.23 R6_2.6.1
## [5] fastmap_1.2.0 cellranger_1.1.0 xfun_0.57 cachem_1.1.0
## [9] knitr_1.51 RCurl_1.98-1.18 htmltools_0.5.9 rmarkdown_2.31
## [13] lifecycle_1.0.5 bitops_1.0-9 cli_3.6.6 sass_0.4.10
## [17] jquerylib_0.1.4 compiler_4.6.1 tools_4.6.1 evaluate_1.0.5
## [21] bslib_0.11.0 yaml_2.3.12 otel_0.2.0 rlang_1.2.0