Source: https://github.com/markziemann/GeneNameErrors2020
View the reports: http://ziemann-lab.net/public/gene_name_errors/
Gene name errors result when data are imported improperly into MS Excel and other spreadsheet programs (Zeeberg et al, 2004). Certain gene names like MARCH3, SEPT2 and DEC1 are converted into date format. These errors are surprisingly common in supplementary data files in the field of genomics (Ziemann et al, 2016). This could be considered a small error because it only affects a small number of genes, however it is symptomtic of poor data processing methods. The purpose of this script is to identify gene name errors present in supplementary files of PubMed Central articles in the previous month.
library("XML")
library("jsonlite")
library("xml2")
library("reutils")
library("readxl")
library("RCurl")Here I will be getting PubMed Central IDs for the previous month.
Start with figuring out the date to search PubMed Central.
CURRENT_MONTH=format(Sys.time(), "%m")
CURRENT_YEAR=format(Sys.time(), "%Y")
if (CURRENT_MONTH == "01") {
PREV_YEAR=as.character(as.numeric(format(Sys.time(), "%Y"))-1)
PREV_MONTH="12"
} else {
PREV_YEAR=CURRENT_YEAR
PREV_MONTH=as.character(as.numeric(format(Sys.time(), "%m"))-1)
}
DATE=paste(PREV_YEAR,"/",PREV_MONTH,sep="")
DATE## [1] "2023/2"Let’s see how many PMC IDs we have in the past month.
QUERY ='((genom*[Abstract]))'
ESEARCH_RES <- esearch(term=QUERY, db = "pmc", rettype = "uilist", retmode = "xml", retstart = 0,
retmax = 5000000, usehistory = TRUE, webenv = NULL, querykey = NULL, sort = NULL, field = NULL,
datetype = NULL, reldate = NULL,
mindate = paste(DATE,"/1",sep="") , maxdate = paste(DATE,"/31",sep=""))
pmc <- efetch(ESEARCH_RES,retmode="text",rettype="uilist",outfile="pmcids.txt")## Retrieving UIDs 1 to 500## Retrieving UIDs 501 to 1000## Retrieving UIDs 1001 to 1500## Retrieving UIDs 1501 to 2000## Retrieving UIDs 2001 to 2500## Retrieving UIDs 2501 to 3000## Retrieving UIDs 3001 to 3500pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 3476writeLines(pmc,con="pmc.txt")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] 6229NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 1316GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 654NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 346ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 245GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC9968710" "PMC9958381" "PMC9957872" "PMC9957247" "PMC9956962"
## [6] "PMC9954656" "PMC9954001" "PMC9953877" "PMC9953556" "PMC9951815"
## [11] "PMC9951354" "PMC9949586" "PMC9948016" "PMC9947504" "PMC9947029"
## [16] "PMC9946837" "PMC9942122" "PMC9938127" "PMC9935838" "PMC9935506"
## [21] "PMC7614190" "PMC9929516" "PMC9928584" "PMC9928580" "PMC9928424"
## [26] "PMC9924891" "PMC9924296" "PMC9922290" "PMC9921068" "PMC9918054"
## [31] "PMC9917645" "PMC9917435" "PMC9916342" "PMC9912572" "PMC9910644"
## [36] "PMC9899606" "PMC9897672" "PMC9882984" "PMC9902559" "PMC9892829"
## [41] "PMC9870088" "PMC9886953" "PMC9968929" "PMC9965082" "PMC9961725"
## [46] "PMC9958104" "PMC9950624" "PMC9950457" "PMC9947337" "PMC9945660"
## [51] "PMC9943656" "PMC9936996" "PMC9939431" "PMC9936472" "PMC9935668"
## [56] "PMC9935575" "PMC9932166" "PMC9932081" "PMC9931374" "PMC9912024"
## [61] "PMC9928207" "PMC9926862" "PMC9926786" "PMC9922817" "PMC9916187"
## [66] "PMC9917439" "PMC9916484" "PMC9916442" "PMC9913674" "PMC9910260"
## [71] "PMC9903843" "PMC9903828" "PMC9903716" "PMC9909915" "PMC9907855"
## [76] "PMC9906884" "PMC9899247" "PMC9894539" "PMC9892568" "PMC9892530"
## [81] "PMC9890215" "PMC9890070" "PMC9889090" "PMC9889089" "PMC9888242"
## [86] "PMC9887306" "PMC9887000" "PMC9883539"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 88ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.2543353Here 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] "PMC9968710 PMC_DL/PMC9968710/supplementaryfiles/41398_2023_2370_MOESM3_ESM.xlsx Hsapiens 25 44818 44817 44621 44813 44624 44625 44817 44805 44627 44817 44626 44622 44815 44626 44624 44625 44809 44896 44623 44815 44817 44815 44809 44621 44626"
## [2] "PMC9968710 PMC_DL/PMC9968710/supplementaryfiles/41398_2023_2370_MOESM3_ESM.xlsx Hsapiens 13 44817 44815 44622 44627 44817 44627 44817 44815 44896 44624 44621 44805 44809"
## [3] "PMC9968710 PMC_DL/PMC9968710/supplementaryfiles/41398_2023_2370_MOESM3_ESM.xlsx Hsapiens 5 44817 44622 44815 44805 44815"
## [4] "PMC9968710 PMC_DL/PMC9968710/supplementaryfiles/41398_2023_2370_MOESM3_ESM.xlsx Hsapiens 7 44624 44805 44625 44622 44817 44815 44815"
## [5] "PMC9968710 PMC_DL/PMC9968710/supplementaryfiles/41398_2023_2370_MOESM3_ESM.xlsx Hsapiens 7 44815 44627 44622 44817 44809 44817 44621"
## [6] "PMC9968710 PMC_DL/PMC9968710/supplementaryfiles/41398_2023_2370_MOESM3_ESM.xlsx Hsapiens 4 44817 44815 44624 44805"
## [7] "PMC9958381 PMC_DL/PMC9958381/supplementaryfiles/mmc10.xlsx Hsapiens 1 44627"
## [8] "PMC9957872 PMC_DL/PMC9957872/supplementaryfiles/NIHMS1859677-supplement-MMC10.xlsx Mmusculus 9 44448 44449 44441 44446 44447 44443 44444 44442 44450"
## [9] "PMC9957247 zip/Table_S6.xlsx Hsapiens 1 44808"
## [10] "PMC9956962 zip/Table_S3_CircRNAs_Information_detected_in_sequence_data_of_hypothalamic_transcriptome_of_Leizhou_Goat.xlsx Hsapiens 13 3-Mar 10-Mar 43532 11-Mar 1-Mar 5-Mar 7-Mar 43714 43526 43713 4-Mar 6-Mar 9-Mar"
## [11] "PMC9954656 zip/Additional_file_S3.xlsx Mmusculus 2 44624 44621"
## [12] "PMC9954656 zip/Additional_file_S3.xlsx Mmusculus 1 44624"
## [13] "PMC9954656 zip/Additional_file_S3.xlsx Mmusculus 1 44986"
## [14] "PMC9954656 zip/Additional_file_S3.xlsx Mmusculus 1 44989"
## [15] "PMC9954001 zip/Table_S5.xlsx Hsapiens 1 44442"
## [16] "PMC9954001 zip/Table_S5.xlsx Hsapiens 1 44442"
## [17] "PMC9953877 zip/cancers-2130992-supplementary/Suppl_material_cancers-2130992_version2/Suppl_Tables_1-3_BC_HGSOC_Cuello_M_Cancers_new.xls Hsapiens 26 44896 44631 44818 44819 44630 44624 44810 44627 44811 44807 44816 44625 44813 44806 44622 44809 44629 44808 44814 44812 44623 44621 44815 44628 44805 44626"
## [18] "PMC9953556 zip/biomolecules-2146911-table_S1.xlsx Hsapiens 1 38961"
## [19] "PMC9951815 PMC_DL/PMC9951815/supplementaryfiles/Table_2.xlsx Hsapiens 1 44531"
## [20] "PMC9951815 PMC_DL/PMC9951815/supplementaryfiles/Table_1.xlsx Hsapiens 27 44257 44442 44443 44257 44446 44445 44262 44450 44264 44451 44259 44256 44261 44453 44447 44263 44441 44531 44265 44258 44440 44266 44448 44444 44256 44449 44260"
## [21] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 2 44079 44089"
## [22] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 4 44262 44262 44445 44449"
## [23] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 9 44446 44442 44450 44454 44447 44445 44257 44449 44441"
## [24] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Ggallus 13 44446 44262 44442 44450 44257 44447 44445 44263 44262 44257 44449 44263 44441"
## [25] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 13 44446 44262 44447 44262 44262 44451 44446 44445 44261 44263 44448 44257 44258"
## [26] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Ggallus 1 44447"
## [27] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 3 44447 44256 44256"
## [28] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 3 44447 44448 44442"
## [29] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 7 44447 44256 44448 44263 44265 44442 44256"
## [30] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 10 44450 44265 44447 44446 44448 44263 44445 44262 44449 44262"
## [31] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 2 44262 44447"
## [32] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 1 44447"
## [33] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 1 44447"
## [34] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 10 44447 44256 44256 44265 44257 44446 44446 44451 44263 44441"
## [35] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 4 44265 44447 44257 44262"
## [36] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 2 44447 44446"
## [37] "PMC9951354 zip/ECE3_9854_SupplementaryTablesS1-S20_RevisedVersion.xlsx Hsapiens 5 44447 44256 44262 44256 44446"
## [38] "PMC9949586 zip/djac160_Supplementary_Data/JNCI-21-1799R2_Jones_Supp_Tables_4-5_081622.xlsx Hsapiens 18 44088 44088 44088 44088 44083 44088 44083 44084 44088 44166 43891 43891 43891 43898 44166 43892 43892 43898"
## [39] "PMC9949586 zip/djac160_Supplementary_Data/JNCI-21-1799R2_Jones_Supp_Tables_4-5_081622.xlsx Hsapiens 17 14-Sep 14-Sep 14-Sep 14-Sep 9-Sep 1-Dec 8-Mar 9-Sep 1-Dec 10-Sep 1-Mar 8-Mar 1-Mar 2-Mar 4-Mar 2-Mar 4-Mar"
## [40] "PMC9948016 PMC_DL/PMC9948016/supplementaryfiles/DataSheet_2.xlsx Hsapiens 3 45178 45178 45178"
## [41] "PMC9947504 PMC_DL/PMC9947504/supplementaryfiles/Table_1.xlsx Hsapiens 26 44806 44813 44628 44819 44627 44815 44809 44621 44625 44811 44626 44624 44816 44807 44818 44805 44896 44630 44808 44631 44810 44629 44814 44812 44622 44623"
## [42] "PMC9947029 PMC_DL/PMC9947029/supplementaryfiles/125_2022_5856_MOESM2_ESM.xlsx Hsapiens 3 37865 39326 42248"
## [43] "PMC9946837 PMC_DL/PMC9946837/supplementaryfiles/41586_2023_5711_MOESM6_ESM.xlsx Mmusculus 1 44448"
## [44] "PMC9946837 PMC_DL/PMC9946837/supplementaryfiles/41586_2023_5711_MOESM6_ESM.xlsx Mmusculus 1 44258"
## [45] "PMC9946837 PMC_DL/PMC9946837/supplementaryfiles/41586_2023_5711_MOESM4_ESM.xlsx Hsapiens 5 43353 43349 43344 43348 43351"
## [46] "PMC9946837 PMC_DL/PMC9946837/supplementaryfiles/41586_2023_5711_MOESM4_ESM.xlsx Hsapiens 2 42985 42987"
## [47] "PMC9946837 PMC_DL/PMC9946837/supplementaryfiles/41586_2023_5711_MOESM4_ESM.xlsx Hsapiens 1 43345"
## [48] "PMC9946837 PMC_DL/PMC9946837/supplementaryfiles/41586_2023_5711_MOESM4_ESM.xlsx Mmusculus 4 43715 43714 43713 43719"
## [49] "PMC9942122 PMC_DL/PMC9942122/supplementaryfiles/mmc5.xlsx Hsapiens 22 43530 43712 43718 43533 43532 43716 43710 43526 43526 43719 43714 43715 43525 43525 43525 43722 43714 43709 43712 43526 43526 43711"
## [50] "PMC9942122 PMC_DL/PMC9942122/supplementaryfiles/mmc5.xlsx Hsapiens 1 44085"
## [51] "PMC9942122 PMC_DL/PMC9942122/supplementaryfiles/mmc5.xlsx Hsapiens 10 43533 43525 43711 43714 43722 43711 43527 43525 43709 43719"
## [52] "PMC9942122 PMC_DL/PMC9942122/supplementaryfiles/mmc5.xlsx Hsapiens 30 43526 43533 43528 43530 43800 43529 43525 43532 43527 43531 43532 43525 43533 43528 43530 43529 43526 43527 43531 43800 43528 43530 43800 43531 43532 43526 43525 43529 43527 43533"
## [53] "PMC9942122 PMC_DL/PMC9942122/supplementaryfiles/mmc5.xlsx Hsapiens 69 43711 43713 43713 43530 43709 43711 43530 43527 43530 43527 43530 43714 43714 43715 43714 43715 43715 43529 43710 43525 43525 43526 43526 43718 43531 43525 43716 43712 43532 43529 43527 43719 43533 43710 43717 43711 43718 43717 43718 43716 43525 43527 43711 43533 43712 43528 43711 43716 43530 43717 43525 43526 43718 43722 43714 43531 43525 43528 43717 43710 43530 43533 43718 43711 43531 43526 43712 43715 43716"
## [54] "PMC9942122 PMC_DL/PMC9942122/supplementaryfiles/mmc6.xlsx Hsapiens 4 43711 43530 43718 43712"
## [55] "PMC9942122 PMC_DL/PMC9942122/supplementaryfiles/mmc4.xlsx Hsapiens 2 44261 44261"
## [56] "PMC9942122 PMC_DL/PMC9942122/supplementaryfiles/mmc7.xlsx Hsapiens 14 44259 44261 44447 44446 44262 44256 44259 44262 44261 44444 44257 44256 44260 44447"
## [57] "PMC9938127 PMC_DL/PMC9938127/supplementaryfiles/41467_2023_36535_MOESM9_ESM.xlsx Hsapiens 105 44819 44819 44622 44622 44622 44621 44621 44621 44628 44628 44628 44625 44625 44625 44625 44629 44816 44816 44805 44805 44805 44808 44808 44630 44630 44630 44630 44630 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44622 44622 44622 44814 44814 44627 44627 44627 44627 44627 44624 44806 44806 44806 44806 44809 44809 44807 44807 44815 44815 44815 44815 44815 44815 44815 44815 44815 44621 44621 44621 44621 44621 44626 44626 44626 44626 44626 44626 44626 44631 44623 44623 44623 44623 44812 44812 44812 44812 44811 44811 44811 44811 44811 44818 44896 44896 44810 44810"
## [58] "PMC9938127 PMC_DL/PMC9938127/supplementaryfiles/41467_2023_36535_MOESM9_ESM.xlsx Hsapiens 218 44819 44819 44819 44819 44819 44622 44622 44622 44622 44622 44622 44622 44621 44621 44621 44621 44621 44628 44628 44628 44628 44625 44625 44625 44625 44625 44629 44629 44629 44816 44816 44816 44816 44816 44805 44805 44805 44805 44805 44805 44805 44805 44805 44805 44805 44805 44808 44808 44808 44808 44808 44808 44808 44808 44808 44630 44630 44630 44630 44630 44630 44630 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44813 44622 44622 44622 44622 44814 44814 44814 44814 44814 44627 44627 44627 44627 44627 44627 44627 44627 44627 44624 44806 44806 44806 44806 44806 44806 44806 44806 44806 44806 44806 44806 44809 44809 44809 44809 44809 44809 44809 44809 44809 44809 44809 44807 44807 44807 44815 44815 44815 44815 44815 44815 44815 44815 44815 44815 44815 44815 44815 44815 44815 44815 44815 44621 44621 44621 44621 44621 44621 44621 44626 44626 44626 44626 44626 44626 44626 44626 44626 44626 44626 44626 44626 44626 44626 44631 44631 44631 44623 44623 44623 44623 44623 44623 44623 44812 44812 44812 44812 44812 44812 44812 44812 44812 44812 44812 44811 44811 44811 44811 44811 44811 44811 44811 44811 44811 44811 44811 44811 44818 44896 44896 44810 44810 44810 44810"
## [59] "PMC9935838 PMC_DL/PMC9935838/supplementaryfiles/Table_2.XLSX Hsapiens 1 44812"
## [60] "PMC9935506 PMC_DL/PMC9935506/supplementaryfiles/41419_2023_5671_MOESM9_ESM.xlsx Mmusculus 1 44449"
## [61] "PMC9935506 PMC_DL/PMC9935506/supplementaryfiles/41419_2023_5671_MOESM9_ESM.xlsx Mmusculus 2 44260 44262"
## [62] "PMC9935506 PMC_DL/PMC9935506/supplementaryfiles/41419_2023_5671_MOESM9_ESM.xlsx Mmusculus 2 44447 44442"
## [63] "PMC9935506 PMC_DL/PMC9935506/supplementaryfiles/41419_2023_5671_MOESM9_ESM.xlsx Mmusculus 2 44441 44257"
## [64] "PMC9935506 PMC_DL/PMC9935506/supplementaryfiles/41419_2023_5671_MOESM10_ESM.xlsx Mmusculus 2 44264 44261"
## [65] "PMC7614190 PMC_DL/PMC7614190/supplementaryfiles/EMS157168-supplement-Supplementary_Tables_1_7.xlsx Hsapiens 1 37316"
## [66] "PMC9929516 PMC_DL/PMC9929516/supplementaryfiles/can-22-2245_table_s2_suppst2.xlsx Hsapiens 25 44624 44622 44815 44806 44814 44621 44623 44626 44811 44805 44627 44812 44810 44625 44622 44628 44807 44808 44621 44630 44813 44629 44896 44818 44816"
## [67] "PMC9929516 PMC_DL/PMC9929516/supplementaryfiles/can-22-2245_table_s2_suppst2.xlsx Hsapiens 23 44807 44621 44629 44630 44813 44812 44628 44627 44625 44806 44810 44623 44805 44626 44815 44814 44811 44622 44624 44622 44621 44896 44808"
## [68] "PMC9928584 PMC_DL/PMC9928584/supplementaryfiles/41556_2022_1059_MOESM3_ESM.xlsx Hsapiens 26 44627 44622 44625 44631 44812 44628 44805 44818 44624 44621 44626 44629 44623 44621 44622 44813 44807 44809 44808 44630 44814 44816 44810 44806 44896 44815"
## [69] "PMC9928584 PMC_DL/PMC9928584/supplementaryfiles/41556_2022_1059_MOESM3_ESM.xlsx Hsapiens 1 44449"
## [70] "PMC9928584 PMC_DL/PMC9928584/supplementaryfiles/41556_2022_1059_MOESM3_ESM.xlsx Hsapiens 26 44621 44813 44621 44622 44631 44627 44629 44815 44630 44808 44805 44809 44623 44806 44624 44625 44896 44807 44814 44622 44816 44810 44818 44812 44626 44628"
## [71] "PMC9928584 PMC_DL/PMC9928584/supplementaryfiles/41556_2022_1059_MOESM3_ESM.xlsx Hsapiens 26 44628 44623 44622 44624 44630 44816 44896 44818 44621 44806 44805 44631 44625 44809 44812 44810 44627 44815 44621 44626 44814 44622 44808 44813 44807 44629"
## [72] "PMC9928584 PMC_DL/PMC9928584/supplementaryfiles/41556_2022_1059_MOESM3_ESM.xlsx Hsapiens 1 44531"
## [73] "PMC9928580 PMC_DL/PMC9928580/supplementaryfiles/Table_1.xlsx Mmusculus 1 44622"
## [74] "PMC9928580 PMC_DL/PMC9928580/supplementaryfiles/Table_1.xlsx Mmusculus 1 44814"
## [75] "PMC9928424 PMC_DL/PMC9928424/supplementaryfiles/elife-80317-supp3.xlsx Mmusculus 16 37865 38231 37135 39326 40057 40787 38596 40422 38961 39692 37500 42248 37012 38108 41883 41153"
## [76] "PMC9928424 PMC_DL/PMC9928424/supplementaryfiles/elife-80317-supp7.xlsx Mmusculus 14 39692 38596 40057 37865 38231 37135 40422 40787 38961 37500 39326 37012 38108 41883"
## [77] "PMC9928424 PMC_DL/PMC9928424/supplementaryfiles/elife-80317-supp2.xlsx Mmusculus 11 37865 39326 37500 38231 40787 37135 40057 38596 39692 38961 40422"
## [78] "PMC9928424 PMC_DL/PMC9928424/supplementaryfiles/elife-80317-supp4.xlsx Mmusculus 11 37865 39326 37500 38231 40787 37135 40057 38596 39692 38961 40422"
## [79] "PMC9928424 PMC_DL/PMC9928424/supplementaryfiles/elife-80317-supp6.xlsx Mmusculus 16 37865 37500 39326 38231 38961 40422 40787 40057 37135 38596 39692 42248 37012 38108 41883 41153"
## [80] "PMC9928424 PMC_DL/PMC9928424/supplementaryfiles/elife-80317-supp5.xlsx Mmusculus 11 37865 39326 37500 38231 40787 37135 40057 38596 39692 38961 40422"
## [81] "PMC9924891 PMC_DL/PMC9924891/supplementaryfiles/12094_2023_3108_MOESM1_ESM.xlsx Hsapiens 4 44622 44621 44805 44810"
## [82] "PMC9924891 PMC_DL/PMC9924891/supplementaryfiles/12094_2023_3108_MOESM1_ESM.xlsx Hsapiens 1 44621"
## [83] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_1_suppst1.xlsx Hsapiens 2 43898 43897"
## [84] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_1_suppst1.xlsx Hsapiens 2 43898 43897"
## [85] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_1_suppst1.xlsx Hsapiens 4 43897 43898 44166 44166"
## [86] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_1_suppst1.xlsx Hsapiens 1 43898"
## [87] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_1_suppst1.xlsx Hsapiens 1 43898"
## [88] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 15 44075 43893 44080 43896 44079 43897 44083 43892 43891 43898 44081 43895 44076 44082 44085"
## [89] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 1 44080"
## [90] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 17 44085 44080 43895 43896 44076 43893 43892 43892 44082 44081 43899 43898 43897 43891 43891 44075 44083"
## [91] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 15 44080 43891 44081 43893 44075 44085 44076 44083 43898 43895 43896 44082 43892 43899 43897"
## [92] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 4 44085 44075 43898 43891"
## [93] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 17 44080 44083 44075 44081 43895 44076 44084 44085 43891 43898 44079 43893 44082 43896 43899 43897 43892"
## [94] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 186 44445 44262 44450 44260 44440 44256 44450 44448 44445 44256 44440 44257 44258 44256 44258 44446 44450 44445 44260 44440 44262 44448 44261 44441 44264 44257 44445 44448 44264 44446 44256 44262 44260 44440 44441 44450 44261 44448 44264 44440 44447 44445 44256 44448 44256 44441 44445 44261 44258 44263 44262 44440 44440 44448 44256 44450 44262 44260 44446 44261 44264 44257 44258 44440 44448 44256 44450 44260 44262 44261 44445 44258 44450 44261 44264 44448 44256 44447 44260 44445 44257 44440 44256 44260 44257 44440 44446 44258 44261 44450 44447 44256 44440 44448 44262 44446 44258 44441 44447 44263 44264 44256 44440 44262 44450 44261 44445 44448 44258 44257 44264 44450 44256 44448 44258 44440 44441 44260 44445 44257 44262 44447 44448 44256 44445 44258 44257 44450 44264 44263 44441 44440 44256 44448 44447 44257 44262 44263 44440 44448 44256 44450 44441 44261 44260 44445 44263 44264 44446 44257 44262 44447 44448 44440 44450 44260 44256 44258 44263 44448 44264 44445 44256 44261 44262 44441 44450 44446 44446 44263 44447 44450 44445 44448 44262 44264 44261 44440 44256 44257 44440 44448 44262 44441 44264 44256"
## [95] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 7 44258 44445 44260 44450 44448 44440 44256"
## [96] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 67 44080 44075 44083 44083 44075 44083 44080 44083 44075 44081 44080 44075 44085 44083 43893 44081 43891 44085 44075 44080 44083 43893 44075 44083 44085 44080 43893 44075 44080 44083 44085 43893 44081 44075 44083 44075 44085 44083 44080 44075 44083 44085 43893 44080 43891 44085 44081 43893 44083 44075 43893 44080 44075 43891 44075 44085 43891 44075 44083 44080 44085 44076 43892 44080 44083 43893 43897"
## [97] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 10 44445 44440 44260 44258 44262 44446 44441 44447 44257 44256"
## [98] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 11 44256 44447 44264 44441 44446 44262 44260 44258 44440 44448 44445"
## [99] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 5 44446 44445 44448 44258 44440"
## [100] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 4 44256 44260 44448 44445"
## [101] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 15 44445 44260 44262 44450 44440 44256 44448 44446 44263 44258 44441 44261 44447 44264 44257"
## [102] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 17 44083 44085 43891 44080 43896 43892 43891 44079 44075 43893 43899 43895 43898 44082 44076 44081 43897"
## [103] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 3 44080 44083 43891"
## [104] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 18 43891 44083 44080 43891 44085 43896 43892 43895 44076 43898 44084 44075 44081 44082 43897 43899 43893 43892"
## [105] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 1 43891"
## [106] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_6_suppst6.xlsx Hsapiens 1 44080"
## [107] "PMC9924296 PMC_DL/PMC9924296/supplementaryfiles/bcd-21-0050_supp.table_3_suppst3.xlsx Hsapiens 1 43898"
## [108] "PMC9922290 PMC_DL/PMC9922290/supplementaryfiles/41467_2023_36462_MOESM16_ESM.xlsx Hsapiens 17 44813 44812 44811 44810 44809 44808 44807 44806 44815 44814 44805 44819 44628 44626 44625 44622 44621"
## [109] "PMC9921068 PMC_DL/PMC9921068/supplementaryfiles/13148_2023_1438_MOESM2_ESM.xlsx Hsapiens 10 37681 40057 40057 37316 37500 38047 40057 36951 38047 40057"
## [110] "PMC9921068 PMC_DL/PMC9921068/supplementaryfiles/13148_2023_1438_MOESM2_ESM.xlsx Hsapiens 3 40787 40057 40057"
## [111] "PMC9921068 PMC_DL/PMC9921068/supplementaryfiles/13148_2023_1438_MOESM2_ESM.xlsx Hsapiens 12 40057 37681 40057 37316 37500 38047 40057 36951 38047 40057 40057 40787"
## [112] "PMC9918054 zip/Table_S1_immune_genes.xlsx Hsapiens 1 44811"
## [113] "PMC9917645 zip/Supplementary_Tables_01_19_2023.xlsx Hsapiens 1 44810"
## [114] "PMC9917645 zip/Supplementary_Tables_01_19_2023.xlsx Hsapiens 1 44815"
## [115] "PMC9917435 PMC_DL/PMC9917435/supplementaryfiles/elife-71235-supp1.xlsx Hsapiens 1 44262"
## [116] "PMC9916342 zip/Source_data_Figure_1.xlsx Hsapiens 3 44628 44627 44629"
## [117] "PMC9912572 PMC_DL/PMC9912572/supplementaryfiles/12885_2022_10491_MOESM3_ESM.xlsx Hsapiens 3 44810 44814 44625"
## [118] "PMC9912572 PMC_DL/PMC9912572/supplementaryfiles/12885_2022_10491_MOESM3_ESM.xlsx Hsapiens 16 44805 44810 44809 44807 44623 44621 44626 44815 44629 44627 44818 44812 44631 44816 44814 44806"
## [119] "PMC9912572 PMC_DL/PMC9912572/supplementaryfiles/12885_2022_10491_MOESM3_ESM.xlsx Hsapiens 3 44623 44808 44815"
## [120] "PMC9912572 PMC_DL/PMC9912572/supplementaryfiles/12885_2022_10491_MOESM3_ESM.xlsx Hsapiens 10 44805 44810 44621 44626 44630 44622 44625 44815 44631 44816"
## [121] "PMC9912572 PMC_DL/PMC9912572/supplementaryfiles/12885_2022_10491_MOESM3_ESM.xlsx Hsapiens 11 44814 44815 44805 44622 44621 44630 44806 44808 44812 44623 44627"
## [122] "PMC9912572 PMC_DL/PMC9912572/supplementaryfiles/12885_2022_10491_MOESM3_ESM.xlsx Hsapiens 12 44813 44807 44622 44805 44814 44629 44808 44809 44626 44628 44625 44811"
## [123] "PMC9912572 PMC_DL/PMC9912572/supplementaryfiles/12885_2022_10491_MOESM3_ESM.xlsx Hsapiens 17 44807 44813 44809 44631 44628 44805 44625 44626 44624 44808 44812 44622 44819 44623 44815 44627 44818"
## [124] "PMC9912572 PMC_DL/PMC9912572/supplementaryfiles/12885_2022_10491_MOESM3_ESM.xlsx Hsapiens 10 44805 44621 44625 44812 44813 44819 44623 44818 44814 44624"