Gene Name Error Monthly Dashboard
Mark Ziemann
2026-07-24
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="2026/1"
#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 4500## Retrieving UIDs 4501 to 5000pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 4675writeLines(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] 80280NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 1670GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 793NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 442ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 330GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC12856215" "PMC12854938" "PMC12857072" "PMC12852518" "PMC12853625"
## [6] "PMC12847017" "PMC12846996" "PMC12839865" "PMC12844564" "PMC12842411"
## [11] "PMC12841099" "PMC12835543" "PMC12837101" "PMC12841453" "PMC12832931"
## [16] "PMC12833344" "PMC12832762" "PMC12830819" "PMC12830518" "PMC12827549"
## [21] "PMC12826143" "PMC12823390" "PMC12824155" "PMC12824682" "PMC12824659"
## [26] "PMC12821903" "PMC12819415" "PMC12820176" "PMC12819441" "PMC12819152"
## [31] "PMC12821805" "PMC12822184" "PMC12820099" "PMC12822518" "PMC12817070"
## [36] "PMC12818872" "PMC7618654" "PMC12815961" "PMC12814444" "PMC12813248"
## [41] "PMC12811338" "PMC12810618" "PMC12810641" "PMC12808549" "PMC12810902"
## [46] "PMC12807715" "PMC12808957" "PMC12808955" "PMC12804938" "PMC12802902"
## [51] "PMC12800067" "PMC12801463" "PMC12801672" "PMC12800293" "PMC12797063"
## [56] "PMC12797436" "PMC12796321" "PMC12796744" "PMC12793829" "PMC12789528"
## [61] "PMC12783525" "PMC12784965" "PMC12781783" "PMC12778141" "PMC12774651"
## [66] "PMC12775020" "PMC12477835" "PMC12769960" "PMC12773779" "PMC12770561"
## [71] "PMC12769673" "PMC12771847" "PMC12771377" "PMC12768487" "PMC12766917"
## [76] "PMC12767815" "PMC12766398" "PMC12765388" "PMC12757036" "PMC12757029"
## [81] "PMC12753682"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 81ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.1832579Look 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] "PMC12856215 zip/Table_S3new.xlsx Hsapiens 23 40422 36951 39692 40057 40787 39873 38412 38777 38231 38961 37681 37500 37316 39142 37865 39326 38596 40238 37135 39508 37316 41153 36951"
## [2] "PMC12856215 zip/Table_S3new.xlsx Hsapiens 22 40422 40057 40787 38231 38412 36951 38596 39326 37316 39692 39142 39873 38777 37316 39508 40238 36951 37681 37865 38961 37135 37500"
## [3] "PMC12856215 zip/Table_S3new.xlsx Hsapiens 22 40057 37865 37500 38777 39873 37681 39508 38596 39326 40238 36951 37316 39142 38412 37135 38961 40422 40787 39692 36951 37316 38231"
## [4] "PMC12856215 zip/Table_S3new.xlsx Hsapiens 203 39692 37500 38777 39326 38412 40787 40787 40057 40057 40057 39142 39142 39142 39142 39142 39142 39142 39142 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37316 37316 37316 42248 42248 42248 42248 42248 38777 38777 39508 39508 40422 40422 40422 39326 36951 37500 39142 39142 37500 37500 39692 37500 38777 39326 39326 39326 39326 38412 38412 40787 40787 37316 39692 36951 40057 40057 40057 40057 37135 39142 39142 39142 39142 39142 39142 39142 39142 39142 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37316 37316 37316 42248 42248 42248 42248 42248 42248 38777 38777 38777 38777 38777 38777 38777 39508 39508 40422 40422 39326 36951 39142 37500 37500 42248 42248 39692 37500 39326 38412 38412 40787 40787 39692 36951 40057 40057 40057 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37316 37316 37316 37316 42248 42248 42248 42248 38777 38777 38777 38777 39508 39508 40422 40422 39326 36951 38412 39142 39142 37500 37500 37500 42248"
## [5] "PMC12856215 zip/Table_S4new.xlsx Mmusculus 20 40422 38047 40057 39142 38231 36951 39326 38412 37316 40787 37135 37500 38777 38961 39873 38596 39508 39692 37681 37316"
## [6] "PMC12856215 zip/Table_S4new.xlsx Mmusculus 114 38231 38231 37500 38231 38231 39692 37500 40422 38412 39508 40787 37316 37500 39142 39508 39142 39142 39142 39142 38596 39142 39508 40787 37316 40422 37316 37500 37500 38412 39142 37500 40787 39142 36951 37500 37316 39142 39142 39142 39508 39326 37135 39326 40057 38231 37500 37500 37500 37500 37500 37500 37500 37500 37316 37316 37316 37316 37316 40422 40422 40422 40422 38412 38412 38412 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 38596 38596 38596 38961 38961 38961 38961 37500 37500 37681 36951 39508 39508 39508 39508 39508 39508 39508 37135 37135 38777 38777 39326 39326 39326 39326 39326 39326 40238 40057 40787 40787 40787 40787 40787 40787 40787 37316 37316"
## [7] "PMC12856215 zip/Table_S2new.xlsx Hsapiens 21 40422 39326 39692 38961 40787 36951 37500 39508 37316 38231 38777 38596 38412 40057 37865 36951 38047 39873 37316 39142 37681"
## [8] "PMC12856215 zip/Table_S2new.xlsx Hsapiens 22 39326 37865 38596 40057 40422 38412 38231 39142 40787 39508 37500 39873 39692 37316 37316 36951 38777 38961 36951 37681 38047 37135"
## [9] "PMC12856215 zip/Table_S2new.xlsx Ggallus 21 37865 40422 38777 39873 38231 36951 37316 38961 40787 39142 39508 39326 38596 37681 39692 37316 36951 40057 37500 38412 38047"
## [10] "PMC12856215 zip/Table_S2new.xlsx Hsapiens 543 40787 36951 37865 42248 40787 37500 37500 38231 38231 36951 37500 37500 42248 37500 37500 40422 37500 38777 37500 38777 39142 40422 38231 37500 37865 40422 39142 37500 37500 38777 39326 39142 38596 39508 37500 37500 42248 37500 40422 37500 39326 37500 37500 40057 40057 39142 38231 37500 38777 37500 39142 37500 37500 38412 39142 38596 38231 40057 38596 37500 38231 39142 37500 38596 40422 37500 39142 39692 38231 37316 37500 37500 38961 37500 40057 37500 40422 38961 38961 38961 37500 37500 37500 37500 37500 37500 40422 37500 37500 37500 38412 38777 38777 39142 39142 39142 37316 37500 37500 40422 38961 40057 39142 37500 39142 37500 37500 40422 39142 39508 37316 37500 40422 38231 37500 42248 37500 37500 37500 38961 42248 37316 38777 39142 42248 40422 39142 38961 38777 37500 37316 39142 37500 39508 37500 37500 37316 42248 37500 37500 38777 37500 37500 37316 39692 39142 37500 37500 37500 37500 38777 38777 38777 37500 38777 38777 38777 37316 37500 37500 38777 37316 37500 38961 39142 37500 38231 38777 39142 38777 37500 37316 38231 38777 37500 37500 38777 40422 37316 37316 37316 37316 37316 36951 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 42248 39508 39508 39508 39508 39508 39508 39508 38412 38412 38412 38412 38412 38412 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 37316 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 40422 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 39142 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 37500 38596 38596 38596 38596 38596 38596 38596 38596 38596 38596 37865 37865 37865 37865 37865 37865 40787 40787 40787 40787 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 39692 39692 39692 39692 39692 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 39326 38961 38961 38961 38961 38961 38961 38961 38961"
## [11] "PMC12854938 PMC_DL/PMC12854938/supplementaryfiles/ALZ-22-e71073-s002.xlsx Hsapiens 3 45723 45723 45723"
## [12] "PMC12857072 PMC_DL/PMC12857072/supplementaryfiles/12711_2025_1025_MOESM5_ESM.xlsx Drerio 1 37865"
## [13] "PMC12852518 PMC_DL/PMC12852518/supplementaryfiles/12672_2026_4470_MOESM6_ESM.xlsx Hsapiens 14 45717 45903 45905 45721 45906 45901 45909 45908 45910 45907 45718 45902 45911 45904"
## [14] "PMC12853625 PMC_DL/PMC12853625/supplementaryfiles/13148_2025_2035_MOESM5_ESM.xlsx Mmusculus 12 45901 45717 45904 45903 45724 45909 45911 45902 45908 45905 45726 45719"
## [15] "PMC12847017 zip/Supplementary_Table_3.xlsx Hsapiens 2 45360 45359"
## [16] "PMC12846996 zip/STable/STable5b.xlsx Hsapiens 1 45726"
## [17] "PMC12839865 zip/Table_S1.xlsx Hsapiens 1 45261"
## [18] "PMC12844564 PMC_DL/PMC12844564/supplementaryfiles/Table3.xlsx Hsapiens 1 45181"
## [19] "PMC12842411 zip/supplementary_material_Tables/supplementary_material_tabS15-16.xls Hsapiens 12 2024/03/07 2024/03/01 2024/03/06 2024/03/03 2024/03/03 2024/03/08 2024/03/08 2024/03/08 2024/04/02 2024/03/02 2024/03/02 2024/03/02"
## [20] "PMC12841099 zip/genes-4063062-supplementary/Supplementary_File/Table_S5.xlsx Athaliana 23 45876 45901 45748 45875 45748 45875 45750 45874 45931 45902 45933 45872 45877 45937 45937 45937 45937 45934 45871 45871 45870 45873 45933"
## [21] "PMC12835543 PMC_DL/PMC12835543/supplementaryfiles/JCSM-17-e70197-s001.xlsx Hsapiens 8 45358 45352 45545 45355 45537 45538 45540 45546"
## [22] "PMC12835543 PMC_DL/PMC12835543/supplementaryfiles/JCSM-17-e70197-s001.xlsx Hsapiens 8 45355 45545 45358 45540 45538 45537 45546 45352"
## [23] "PMC12835543 PMC_DL/PMC12835543/supplementaryfiles/JCSM-17-e70197-s001.xlsx Hsapiens 8 45537 45546 45358 45545 45355 45538 45540 45352"
## [24] "PMC12835543 PMC_DL/PMC12835543/supplementaryfiles/JCSM-17-e70197-s001.xlsx Hsapiens 8 45355 45358 45546 45537 45540 45538 45545 45352"
## [25] "PMC12835543 PMC_DL/PMC12835543/supplementaryfiles/JCSM-17-e70197-s001.xlsx Hsapiens 1 45354"
## [26] "PMC12835543 PMC_DL/PMC12835543/supplementaryfiles/JCSM-17-e70197-s001.xlsx Hsapiens 2 45543 45543"
## [27] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 6 45722 45909 45907 45911 45723 45721"
## [28] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 3 45722 45906 45911"
## [29] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 2 45908 45907"
## [30] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 3 45722 45911 45723"
## [31] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 2 45722 45906"
## [32] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 7 45903 45910 45722 45906 45907 45911 45721"
## [33] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 2 45723 45722"
## [34] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Ggallus 3 45906 45722 45903"
## [35] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 5 45911 45907 45722 45723 45721"
## [36] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Ggallus 2 45722 45909"
## [37] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 1 45722"
## [38] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 6 45722 45907 45911 45721 45723 45906"
## [39] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 3 45907 45722 45909"
## [40] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 2 45911 45722"
## [41] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 1 45911"
## [42] "PMC12837101 PMC_DL/PMC12837101/supplementaryfiles/13287_2025_4843_MOESM6_ESM.xlsx Hsapiens 3 45722 45911 45909"
## [43] "PMC12841453 PMC_DL/PMC12841453/supplementaryfiles/NIHMS2125819-supplement-3.xlsx Drerio 10 45550 45545 45541 45537 45357 45353 45359 45356 45538 45547"
## [44] "PMC12841453 PMC_DL/PMC12841453/supplementaryfiles/NIHMS2125819-supplement-3.xlsx Drerio 10 45538 45356 45547 45359 45545 45541 45550 45537 45353 45357"
## [45] "PMC12841453 PMC_DL/PMC12841453/supplementaryfiles/NIHMS2125819-supplement-3.xlsx Drerio 10 45547 45538 45356 45359 45353 45541 45537 45357 45550 45545"
## [46] "PMC12841453 PMC_DL/PMC12841453/supplementaryfiles/NIHMS2125819-supplement-3.xlsx Drerio 10 45537 45353 45538 45357 45541 45545 45550 45547 45356 45359"
## [47] "PMC12841453 PMC_DL/PMC12841453/supplementaryfiles/NIHMS2125819-supplement-3.xlsx Drerio 10 45359 45538 45357 45353 45356 45537 45541 45545 45550 45547"
## [48] "PMC12841453 PMC_DL/PMC12841453/supplementaryfiles/NIHMS2125819-supplement-2.xlsx Drerio 14 45550 45353 45545 45567 45541 45357 45537 45359 45538 45356 45547 45539 45362 45352"
## [49] "PMC12832931 PMC_DL/PMC12832931/supplementaryfiles/Table1.xlsx Mmusculus 25 45549 45550 45362 45352 45546 45357 45355 45358 45354 45544 45360 45540 45545 45353 45543 45356 45361 45359 45539 45536 45542 45538 45547 45541 45537"
## [50] "PMC12832931 PMC_DL/PMC12832931/supplementaryfiles/Table1.xlsx Mmusculus 25 45543 45360 45353 45352 45537 45538 45355 45544 45547 45362 45539 45549 45354 45356 45546 45357 45545 45361 45536 45541 45359 45358 45540 45542 45550"
## [51] "PMC12832931 PMC_DL/PMC12832931/supplementaryfiles/Table1.xlsx Mmusculus 25 45354 45546 45547 45352 45549 45355 45358 45359 45360 45543 45545 45357 45540 45356 45544 45550 45536 45361 45362 45542 45541 45539 45538 45353 45537"
## [52] "PMC12833344 PMC_DL/PMC12833344/supplementaryfiles/Table4.xlsx Hsapiens 2 45173 44992"
## [53] "PMC12833344 PMC_DL/PMC12833344/supplementaryfiles/Table4.xlsx Hsapiens 3 44987 45173 44995"
## [54] "PMC12832762 PMC_DL/PMC12832762/supplementaryfiles/Table2.xlsx Hsapiens 1 45727"
## [55] "PMC12830819 PMC_DL/PMC12830819/supplementaryfiles/41467_2025_67633_MOESM3_ESM.xlsx Hsapiens 6 45723 45724 45722 45725 45721 45915"
## [56] "PMC12830819 PMC_DL/PMC12830819/supplementaryfiles/41467_2025_67633_MOESM3_ESM.xlsx Hsapiens 22 45915 45724 45915 45723 45722 45722 45915 45725 45915 45724 45721 45724 45725 45721 45721 45724 45722 45723 45722 45721 45725 45725"
## [57] "PMC12830819 PMC_DL/PMC12830819/supplementaryfiles/41467_2025_67633_MOESM3_ESM.xlsx Hsapiens 6 45723 45722 45721 45725 45724 45915"
## [58] "PMC12830819 PMC_DL/PMC12830819/supplementaryfiles/41467_2025_67633_MOESM3_ESM.xlsx Hsapiens 24 45723 45722 45724 45725 45724 45722 45915 45723 45721 45721 45725 45915 45721 45723 45915 45724 45722 45722 45723 45725 45915 45724 45725 45721"
## [59] "PMC12830819 PMC_DL/PMC12830819/supplementaryfiles/41467_2025_67633_MOESM5_ESM.xlsx Hsapiens 36 45717 45717 45718 45718 45721 45721 45722 45722 45723 45723 45724 45724 45725 45725 45915 45915 45910 45910 45911 45911 45902 45902 45903 45903 45905 45905 45905 45905 45906 45906 45907 45907 45908 45908 45909 45909"
## [60] "PMC12830819 PMC_DL/PMC12830819/supplementaryfiles/41467_2025_67633_MOESM6_ESM.xlsx Hsapiens 34 45908 45915 45911 45905 45725 45910 45722 45903 45909 45907 45724 45718 45721 45717 45722 45908 45915 45905 45725 45907 45910 45911 45724 45903 45902 45906 45718 45717 45906 45723 45721 45909 45905 45902"
## [61] "PMC12830819 PMC_DL/PMC12830819/supplementaryfiles/41467_2025_67633_MOESM6_ESM.xlsx Hsapiens 12 45723 45722 45915 45724 45723 45722 45724 45721 45725 45915 45725 45721"
## [62] "PMC12830518 PMC_DL/PMC12830518/supplementaryfiles/12672_2025_4277_MOESM6_ESM.xlsx Hsapiens 1 45353"
## [63] "PMC12827549 PMC_DL/PMC12827549/supplementaryfiles/Table8.xlsx Hsapiens 6 45173 45180 44988 45078 45016 11749"
## [64] "PMC12827549 PMC_DL/PMC12827549/supplementaryfiles/Table8.xlsx Hsapiens 7 45173 45180 45180 44988 44988 45180 44988"
## [65] "PMC12826143 PMC_DL/PMC12826143/supplementaryfiles/hc9-10-e0884-s002.xlsx Hsapiens 25 7-Sep 2-Mar 9-Mar 5-Mar 6-Sep 1-Dec 1-Mar 1-Sep 10-Mar 10-Sep 11-Mar 11-Sep 12-Sep 14-Sep 2-Sep 3-Mar 3-Sep 4-Mar 4-Sep 5-Sep 6-Mar 7-Mar 8-Mar 8-Sep 9-Sep"
## [66] "PMC12823390 PMC_DL/PMC12823390/supplementaryfiles/41591_2025_3999_MOESM4_ESM.xlsx Hsapiens 3 44814 44807 44805"
## [67] "PMC12823390 PMC_DL/PMC12823390/supplementaryfiles/41591_2025_3999_MOESM4_ESM.xlsx Hsapiens 1 45721"
## [68] "PMC12823390 PMC_DL/PMC12823390/supplementaryfiles/41591_2025_3999_MOESM4_ESM.xlsx Hsapiens 1 45721"
## [69] "PMC12824155 PMC_DL/PMC12824155/supplementaryfiles/41386_2025_2255_MOESM2_ESM.xlsx Hsapiens 28 45719 45903 45910 45726 45992 45722 45914 45904 45907 45909 45723 45905 45908 45912 45901 45911 45717 45901 45725 45717 45902 45720 45915 45718 45727 45724 45721 45718"
## [70] "PMC12824155 PMC_DL/PMC12824155/supplementaryfiles/41386_2025_2255_MOESM2_ESM.xlsx Hsapiens 28 45719 45910 45722 45903 45912 45992 45914 45726 45908 45907 45723 45727 45901 45904 45909 45725 45915 45901 45905 45720 45718 45902 45717 45911 45718 45717 45724 45721"
## [71] "PMC12824682 PMC_DL/PMC12824682/supplementaryfiles/BLOOD_BLD-2025-028954-mmc2.xlsx Hsapiens 8 45537 45357 45542 45358 45541 45546 45356 45544"
## [72] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45536"
## [73] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45540"
## [74] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 2 45359 45354"
## [75] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 2 45359 45354"
## [76] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45353"
## [77] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45354"
## [78] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45357"
## [79] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45352"
## [80] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45352"
## [81] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45360"
## [82] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45352"
## [83] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45352"
## [84] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45352"
## [85] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45352"
## [86] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45360"
## [87] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45360"
## [88] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 2 45360 45352"
## [89] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45356"
## [90] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 1 45354"
## [91] "PMC12824659 PMC_DL/PMC12824659/supplementaryfiles/BLOOD_BLD-2024-027692-mmc9.xlsx Hsapiens 2 45356 45354"
## [92] "PMC12821903 PMC_DL/PMC12821903/supplementaryfiles/12864_2025_12418_MOESM2_ESM.xlsx Hsapiens 2 45903 45904"
## [93] "PMC12819415 PMC_DL/PMC12819415/supplementaryfiles/41392_2025_2547_MOESM3_ESM.xlsx Hsapiens 3 45359 45360 45354"
## [94] "PMC12820176 PMC_DL/PMC12820176/supplementaryfiles/41467_2026_68330_MOESM18_ESM.xlsx Scerevisiae 103 36982 37165 36982 37165 36982 37165 36982 37165 36982 36982 37165 36982 37165 37165 36982 36982 37165 36982 37165 36982 37165 36982 37165 37165 36982 37165 36982 37165 36982 36982 36982 36982 37165 37165 36982 36982 37165 37165 37165 37165 36982 37165 36982 37165 36982 37165 37165 36982 36982 37165 36982 37165 36982 37165 37165 36982 37165 36982 36982 37165 37165 36982 36982 37165 36982 37165 36982 37165 37165 36982 36982 37165 36982 37165 36982 37165 36982 37165 36982 37165 36982 37165 36982 37165 36982 36982 37165 36982 36982 37165 36982 37165 36982 37165 36982 37165 36982 36982 37165 36982 37165 36982 37165"
## [95] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 1 45717"
## [96] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 2 45717 45721"
## [97] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 8 45718 45992 45720 45721 45726 45719 45915 45723"
## [98] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 3 45720 45724 45723"
## [99] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 1 45720"
## [100] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 5 45992 45717 45721 45720 45726"
## [101] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 5 45992 45721 45717 45720 45726"
## [102] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 5 45992 45721 45717 45725 45720"
## [103] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 6 45992 45721 45725 45720 45717 45724"
## [104] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 2 45718 45722"
## [105] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 1 45718"
## [106] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 3 45718 45724 45722"
## [107] "PMC12819441 PMC_DL/PMC12819441/supplementaryfiles/10238_2025_1985_MOESM1_ESM.xlsx Hsapiens 2 45723 45720"
## [108] "PMC12819152 PMC_DL/PMC12819152/supplementaryfiles/41594_2025_1731_MOESM4_ESM.xlsx Dmelanogaster 4 45171 45173 45174 45261"
## [109] "PMC12819152 PMC_DL/PMC12819152/supplementaryfiles/41594_2025_1731_MOESM4_ESM.xlsx Dmelanogaster 5 45901 45904 45905 45992 45902"
## [110] "PMC12821805 PMC_DL/PMC12821805/supplementaryfiles/12885_2025_15341_MOESM11_ESM.xlsx Hsapiens 1 45353"
## [111] "PMC12822184 PMC_DL/PMC12822184/supplementaryfiles/13046_2025_3586_MOESM4_ESM.xlsx Hsapiens 24 45725 45908 45907 45902 45992 45909 45905 45911 45723 45722 45915 45904 45912 45719 45727 45903 45910 45718 45720 45726 45914 45721 45724 45906"
## [112] "PMC12822184 PMC_DL/PMC12822184/supplementaryfiles/13046_2025_3586_MOESM4_ESM.xlsx Hsapiens 24 45909 45906 45724 45721 45723 45914 45992 45912 45719 45726 45720 45915 45718 45722 45910 45904 45911 45907 45727 45908 45902 45903 45905 45725"
## [113] "PMC12820099 PMC_DL/PMC12820099/supplementaryfiles/41467_2025_67438_MOESM4_ESM.xlsx Mmusculus 1 19184"
## [114] "PMC12822518 PMC_DL/PMC12822518/supplementaryfiles/NIHMS2128202-supplement-2.xlsx Hsapiens 45 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360"
## [115] "PMC12822518 PMC_DL/PMC12822518/supplementaryfiles/NIHMS2128202-supplement-2.xlsx Hsapiens 45 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360"
## [116] "PMC12822518 PMC_DL/PMC12822518/supplementaryfiles/NIHMS2128202-supplement-2.xlsx Hsapiens 54 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360"
## [117] "PMC12822518 PMC_DL/PMC12822518/supplementaryfiles/NIHMS2128202-supplement-2.xlsx Hsapiens 54 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360"
## [118] "PMC12822518 PMC_DL/PMC12822518/supplementaryfiles/NIHMS2128202-supplement-2.xlsx Hsapiens 54 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360 45352 45352 45353 45354 45356 45357 45358 45359 45360"
## [119] "PMC12822518 PMC_DL/PMC12822518/supplementaryfiles/NIHMS2128202-supplement-2.xlsx Hsapiens 13 45352 45353 45352 45361 45362 45353 45354 45355 45356 45357 45358 45359 45360"
## [120] "PMC12822518 PMC_DL/PMC12822518/supplementaryfiles/NIHMS2128202-supplement-2.xlsx Hsapiens 13 45352 45353 45352 45361 45362 45353 45354 45355 45356 45357 45358 45359 45360"
## [121] "PMC12822518 PMC_DL/PMC12822518/supplementaryfiles/NIHMS2128202-supplement-2.xlsx Hsapiens 13 45352 45353 45352 45361 45362 45353 45354 45355 45356 45357 45358 45359 45360"
## [122] "PMC12817070 zip/Supplementary_Tables.xlsx Mmusculus 31 45903 45722 45908 45907 45911 45720 45725 45906 45905 45727 45717 45721 45901 22525 45723 45909 45904 26177 29830 45724 45910 45718 45809 45728 45902 45718 45810 45729 33482 29646 26543"
## [123] "PMC12817070 zip/Supplementary_Tables.xlsx Rnorvegicus 31 45903 45722 45908 45907 45911 45720 45725 45906 45905 45727 45717 45721 45901 45906 45723 45909 45904 45907 45908 45724 45910 45718 45717 45902 45718 45717 45909 45910 45911 45724 45907"
## [124] "PMC12817070 zip/Supplementary_Tables.xlsx Hsapiens 28 45915 45718 45717 45724 45721 45725 45912 45901 45904 45726 45909 45718 45910 45723 45720 45902 45905 45903 45911 45717 45722 45727 45719 45908 45907 45914 45992 45906"
## [125] "PMC12818872 PMC_DL/PMC12818872/supplementaryfiles/elife-107161-supp2.xlsx Mmusculus 2 45546 45546"
## [126] "PMC7618654 PMC_DL/PMC7618654/supplementaryfiles/EMS212078-supplement-Source_Data_Extended_Data_Figure_5.xlsx Mmusculus 3 39326 37316 37500"
## [127] "PMC7618654 PMC_DL/PMC7618654/supplementaryfiles/EMS212078-supplement-Source_Data_Figure_2.xlsx Mmusculus 6 40422 40057 40787 39692 39326 37500"
## [128] "PMC7618654 PMC_DL/PMC7618654/supplementaryfiles/EMS212078-supplement-Source_Data_Figure_2.xlsx Mmusculus 8 38412 40787 40422 37135 40057 37316 39326 37500"
## [129] "PMC7618654 PMC_DL/PMC7618654/supplementaryfiles/EMS212078-supplement-Source_Data_Figure_2.xlsx Mmusculus 8 40787 38412 40422 37135 40057 37316 39326 37500"
## [130] "PMC7618654 PMC_DL/PMC7618654/supplementaryfiles/EMS212078-supplement-Source_Data_Figure_2.xlsx Mmusculus 8 40787 38412 40422 37135 40057 37316 39326 37500"
## [131] "PMC12815961 PMC_DL/PMC12815961/supplementaryfiles/41698_2025_1235_MOESM2_ESM.xlsx Hsapiens 1 45902"
## [132] "PMC12814444 zip/Springer,Fleck_et_al_supplemental_data_final/Data_S14-List_of_expressed_genes_per_cell_line,_related_to_Figure_3.xlsx Hsapiens 2 45352 45353"
## [133] "PMC12814444 zip/Springer,Fleck_et_al_supplemental_data_final/Data_S14-List_of_expressed_genes_per_cell_line,_related_to_Figure_3.xlsx Hsapiens 1 45353"
## [134] "PMC12814444 zip/Springer,Fleck_et_al_supplemental_data_final/Data_S14-List_of_expressed_genes_per_cell_line,_related_to_Figure_3.xlsx Hsapiens 2 45352 45353"
## [135] "PMC12813248 PMC_DL/PMC12813248/supplementaryfiles/mmc5.xlsx Hsapiens 28 45717 45718 45901 45906 45723 45907 45717 45718 45915 45720 45992 45722 45908 45904 45721 45914 45727 45910 45902 45719 45726 45903 45724 45905 45725 45909 45911 45912"
## [136] "PMC12813248 PMC_DL/PMC12813248/supplementaryfiles/mmc6.xlsx Hsapiens 28 45992 45717 45718 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"
## [137] "PMC12813248 PMC_DL/PMC12813248/supplementaryfiles/mmc2.xlsx Hsapiens 1 45722"
## [138] "PMC12811338 PMC_DL/PMC12811338/supplementaryfiles/44318_2025_647_MOESM3_ESM.xlsx Scerevisiae 3 37165 37165 37165"
## [139] "PMC12810618 zip/aeb4348_table_s2.xlsx Hsapiens 54 44260 44440 44448 44262 44443 44446 44266 44259 44453 44445 44265 44256 44256 44256 44256 44447 44444 44449 44257 44257 44257 44257 44256 44256 44256 44256 44257 44257 44257 44257 44257 44257 44257 44257 44257 44257 44257 44257 44256 44256 44256 44256 44531 44256 44256 44256 44256 44451 44258 44261 44450 44441 44442 44264"
## [140] "PMC12810618 zip/aeb4348_table_s2.xlsx Hsapiens 54 44447 44258 44265 44449 44256 44256 44256 44256 44256 44256 44256 44256 44257 44257 44257 44257 44450 44256 44256 44256 44256 44257 44257 44257 44257 44256 44256 44256 44256 44257 44257 44257 44257 44266 44440 44442 44446 44257 44257 44257 44257 44453 44261 44262 44448 44451 44531 44259 44441 44445 44260 44444 44443 44264"
## [141] "PMC12810641 zip/adw7667_tables_s1_to_s16.xlsx Mmusculus 1 45905"
## [142] "PMC12810641 zip/adw7667_tables_s1_to_s16.xlsx Mmusculus 1 45907"
## [143] "PMC12810641 zip/adw7667_tables_s1_to_s16.xlsx Mmusculus 1 45905"
## [144] "PMC12810641 zip/adw7667_tables_s1_to_s16.xlsx Mmusculus 1 45907"
## [145] "PMC12810641 zip/adw7667_tables_s1_to_s16.xlsx Ggallus 9 45172 45172 45172 45172 45172 45172 45172 45172 45172"
## [146] "PMC12810641 zip/adw7667_tables_s1_to_s16.xlsx Mmusculus 2 45905 45907"
## [147] "PMC12810641 zip/adw7667_tables_s1_to_s16.xlsx Mmusculus 2 45905 45907"
## [148] "PMC12808549 zip/Data_S1.xlsx Hsapiens 1 37865"
## [149] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s010.xlsx Hsapiens 27 45353 45538 45539 45353 45542 45541 45358 45546 45360 45547 45355 45352 45357 45549 45543 45359 45537 45627 45361 45354 45536 45362 45544 45540 45352 45545 45356"
## [150] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s010.xlsx Hsapiens 17 45354 45545 45359 45543 45546 45356 45357 45360 45352 45353 45542 45358 45541 45537 45353 45352 45544"
## [151] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s010.xlsx Hsapiens 17 45354 45359 45545 45543 45546 45356 45360 45357 45352 45353 45358 45542 45537 45353 45541 45352 45544"
## [152] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s010.xlsx Hsapiens 17 45543 45359 45545 45356 45354 45546 45357 45360 45352 45542 45353 45541 45537 45358 45352 45353 45544"
## [153] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s010.xlsx Hsapiens 17 45543 45541 45359 45360 45358 45356 45537 45352 45352 45353 45545 45353 45544 45357 45354 45542 45546"
## [154] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s010.xlsx Hsapiens 17 45356 45357 45352 45537 45358 45543 45359 45541 45352 45544 45542 45546 45360 45353 45354 45353 45545"
## [155] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s010.xlsx Hsapiens 17 45357 45541 45537 45543 45542 45356 45545 45352 45359 45546 45354 45358 45360 45353 45544 45353 45352"
## [156] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s010.xlsx Hsapiens 17 45545 45360 45544 45542 45546 45352 45353 45356 45537 45353 45352 45357 45543 45359 45354 45358 45541"
## [157] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s015.xlsx Hsapiens 17 44626 44812 44625 44627 44811 44623 44815 44622 44628 44621 44806 44814 44813 44629 44621 44623 44622"
## [158] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s016.xlsx Hsapiens 4 45627 45627 45627 45353"
## [159] "PMC12810902 PMC_DL/PMC12810902/supplementaryfiles/pgen.1011983.s016.xlsx Hsapiens 25 45353 45353 45353 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45627 45353"
## [160] "PMC12807715 zip/Supplementary_Table_S2.xlsx Hsapiens 3 45903 45904 45717"
## [161] "PMC12808957 PMC_DL/PMC12808957/supplementaryfiles/mmc2.xlsx Hsapiens 2 45903 45903"
## [162] "PMC12808955 PMC_DL/PMC12808955/supplementaryfiles/NIHMS2115151-supplement-MMC2.xlsx Hsapiens 4 45902 45723 45723 45902"
## [163] "PMC12808955 PMC_DL/PMC12808955/supplementaryfiles/NIHMS2115151-supplement-MMC2.xlsx Hsapiens 1 45723"
## [164] "PMC12808955 PMC_DL/PMC12808955/supplementaryfiles/NIHMS2115151-supplement-MMC2.xlsx Hsapiens 1 45723"
## [165] "PMC12808955 PMC_DL/PMC12808955/supplementaryfiles/NIHMS2115151-supplement-MMC2.xlsx Hsapiens 1 45909"
## [166] "PMC12808955 PMC_DL/PMC12808955/supplementaryfiles/NIHMS2115151-supplement-MMC2.xlsx Hsapiens 7 45909 45911 45906 45911 45911 45906 45907"
## [167] "PMC12804938 PMC_DL/PMC12804938/supplementaryfiles/41467_2025_67236_MOESM4_ESM.xlsx Hsapiens 24 45902 45904 45907 45724 45908 45727 45722 45721 45912 45915 45909 45910 45903 45992 45720 45726 45905 45723 45719 45906 45718 45914 45725 45911"
## [168] "PMC12804938 PMC_DL/PMC12804938/supplementaryfiles/41467_2025_67236_MOESM4_ESM.xlsx Hsapiens 24 45721 45904 45907 45725 45908 45722 45915 45724 45902 45909 45912 45905 45718 45727 45992 45723 45726 45719 45903 45914 45720 45911 45906 45910"
## [169] "PMC12804938 PMC_DL/PMC12804938/supplementaryfiles/41467_2025_67236_MOESM4_ESM.xlsx Hsapiens 24 45721 45904 45907 45725 45908 45722 45915 45724 45902 45909 45912 45905 45718 45727 45914 45992 45723 45726 45719 45903 45720 45911 45906 45910"
## [170] "PMC12802902 zip/Table_S4.xlsx Hsapiens 4 45725 45717 45911 45719"
## [171] "PMC12800067 PMC_DL/PMC12800067/supplementaryfiles/41467_2025_67154_MOESM2_ESM.xlsx Hsapiens 27 45915 45720 45905 45909 45721 45718 45722 45903 45723 45902 45907 45719 45717 45911 45901 45912 45718 45908 45725 45727 45717 45992 45724 45910 45726 45904 45914"
## [172] "PMC12801463 PMC_DL/PMC12801463/supplementaryfiles/12935_2025_4093_MOESM1_ESM.xlsx Hsapiens 34 Legend: A total of 77 unique genes from 27 articles were retrieved from the literature search performed on 24-10-2024 using the search query “uveal melanoma AND (epigenetics OR DNA methylation or cfDNA or ctDNA)”."
## [173] "PMC12801672 PMC_DL/PMC12801672/supplementaryfiles/13073_2025_1590_MOESM2_ESM.xlsx Hsapiens 22 44992 45171 45179 44990 45176 45180 44987 45175 44993 45177 45174 45174 44991 44988 45184 44986 44994 44986 45173 44987 45170 45178"
## [174] "PMC12800293 PMC_DL/PMC12800293/supplementaryfiles/41467_2025_67171_MOESM4_ESM.xlsx Hsapiens 21 3-Sep 10-Sep 6-Mar 1-Mar 8-Mar 7-Sep 7-Mar 9-Sep 10-Mar 4-Sep 5-Mar 5-Sep 9-Mar 1-Sep 2-Sep 8-Sep 2-Mar 15-Sep 6-Sep 11-Sep 3-Mar"
## [175] "PMC12800293 PMC_DL/PMC12800293/supplementaryfiles/41467_2025_67171_MOESM4_ESM.xlsx Hsapiens 15 45722 45723 45724 45907 45909 45725 45906 45902 45718 45721 45908 45901 45719 45915 45911"
## [176] "PMC12797063 PMC_DL/PMC12797063/supplementaryfiles/mmc2.xlsx Hsapiens 12 45723 45722 45992 45719 45721 45727 45726 45725 45718 45720 45724 45717"
## [177] "PMC12797436 PMC_DL/PMC12797436/supplementaryfiles/12915_2025_2485_MOESM5_ESM.xlsx Dmelanogaster 1 45627"
## [178] "PMC12797436 PMC_DL/PMC12797436/supplementaryfiles/12915_2025_2485_MOESM12_ESM.xlsx Dmelanogaster 1 45627"
## [179] "PMC12797436 PMC_DL/PMC12797436/supplementaryfiles/12915_2025_2485_MOESM12_ESM.xlsx Dmelanogaster 1 45627"
## [180] "PMC12797436 PMC_DL/PMC12797436/supplementaryfiles/12915_2025_2485_MOESM8_ESM.xlsx Dmelanogaster 1 45627"
## [181] "PMC12797436 PMC_DL/PMC12797436/supplementaryfiles/12915_2025_2485_MOESM10_ESM.xlsx Dmelanogaster 1 45992"
## [182] "PMC12797436 PMC_DL/PMC12797436/supplementaryfiles/12915_2025_2485_MOESM3_ESM.xlsx Dmelanogaster 5 45627 45536 45537 45540 45539"
## [183] "PMC12796321 PMC_DL/PMC12796321/supplementaryfiles/41467_2025_67107_MOESM3_ESM.xlsx Hsapiens 1 38047"
## [184] "PMC12796744 PMC_DL/PMC12796744/supplementaryfiles/mmc3.xlsx Mmusculus 2 45170 45173"
## [185] "PMC12796744 PMC_DL/PMC12796744/supplementaryfiles/mmc3.xlsx Mmusculus 2 45170 45173"
## [186] "PMC12796744 PMC_DL/PMC12796744/supplementaryfiles/mmc3.xlsx Mmusculus 2 45170 45173"
## [187] "PMC12793829 PMC_DL/PMC12793829/supplementaryfiles/Supplementary_Data5.xlsx Hsapiens 14 45353 45546 45544 45352 45543 45542 45537 45549 45538 45547 45536 45539 45541 45545"
## [188] "PMC12789528 PMC_DL/PMC12789528/supplementaryfiles/41467_2025_64954_MOESM4_ESM.xlsx Hsapiens 28 44991 45171 45183 44994 45172 44996 44986 45173 44987 45261 45181 44995 45174 45176 44993 45170 45184 44986 45178 44989 45170 44990 45177 44992 45179 45180 44987 44988"
## [189] "PMC12783525 zip/Supplementary_Tables.xlsx Hsapiens 28 45903 45901 45901 45901 45901 45901 45901 45901 45901 45901 45901 45901 45723 45901 45901 45901 45901 45901 45901 45901 45901 45723 45901 45901 45903 45723 45723 45723"
## [190] "PMC12784965 PMC_DL/PMC12784965/supplementaryfiles/supplementary_table_bbaf694.xlsx Hsapiens 2 45720 45724"
## [191] "PMC12784965 PMC_DL/PMC12784965/supplementaryfiles/supplementary_table_bbaf694.xlsx Hsapiens 23 45627 45539 45540 45541 45544 45353 45352 45361 45353 45354 45355 45356 45357 45358 45359 45360 45546 45547 45550 45537 45538 45542 45543"
## [192] "PMC12784965 zip/Supplementary_materials_bbaf694_Table.xlsx Hsapiens 2 45720 45724"
## [193] "PMC12784965 zip/Supplementary_materials_bbaf694_Table.xlsx Hsapiens 23 45627 45539 45540 45541 45544 45353 45352 45361 45353 45354 45355 45356 45357 45358 45359 45360 45546 45547 45550 45537 45538 45542 45543"
## [194] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 2-Sep"
## [195] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 3 6-Mar 7-Mar 6-Sep"
## [196] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 2 3-Mar 10-Sep"
## [197] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 3 3-Mar 11-Sep 8-Sep"
## [198] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 11-Sep"
## [199] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 11-Sep"
## [200] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 2 10-Sep 6-Sep"
## [201] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 4 3-Mar 6-Sep 1-Mar 7-Mar"
## [202] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 2 10-Sep 6-Mar"
## [203] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 11-Sep"
## [204] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 11-Sep"
## [205] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 3-Mar"
## [206] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 10-Sep"
## [207] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 10-Sep"
## [208] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 2 5-Mar 3-Mar"
## [209] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 8-Sep"
## [210] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 2 8-Sep 6-Sep"
## [211] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 1 6-Sep"
## [212] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 3 3-Mar 8-Sep 2-Mar"
## [213] "PMC12781783 zip/Table_S8_top1000_PI3KAUC.xlsx Hsapiens 2 3-Mar 1-Mar"
## [214] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 2-Sep"
## [215] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 3 6-Mar 7-Mar 6-Sep"
## [216] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 2 3-Mar 10-Sep"
## [217] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 3-Mar"
## [218] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 11-Sep"
## [219] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 3 3-Mar 6-Sep 7-Sep"
## [220] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 11-Sep"
## [221] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 2 10-Sep 6-Sep"
## [222] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 2 6-Sep 1-Mar"
## [223] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 2 10-Sep 6-Mar"
## [224] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 11-Sep"
## [225] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 10-Sep"
## [226] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 3-Mar"
## [227] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 10-Sep"
## [228] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 10-Sep"
## [229] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 3 3-Mar 6-Sep 7-Sep"
## [230] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 2 5-Mar 3-Mar"
## [231] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 3-Mar"
## [232] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 2 6-Sep 3-Mar"
## [233] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 3-Mar"
## [234] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 6-Sep"
## [235] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 3 3-Mar 2-Mar 8-Sep"
## [236] "PMC12781783 zip/Table_S6_top1000_ERKAUC.xlsx Hsapiens 1 11-Sep"
## [237] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 3-Mar"
## [238] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 2 3-Mar 10-Sep"
## [239] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 3-Mar"
## [240] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 2 2-Sep 8-Sep"
## [241] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 2 6-Mar 6-Sep"
## [242] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 2 10-Sep 3-Mar"
## [243] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 3-Mar"
## [244] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 2 6-Mar 11-Sep"
## [245] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 7-Mar"
## [246] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 6-Sep"
## [247] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 4 3-Mar 7-Mar 1-Mar 6-Sep"
## [248] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 2 10-Sep 3-Mar"
## [249] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 3-Mar"
## [250] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 10-Sep"
## [251] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 6-Sep"
## [252] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 3 10-Sep 3-Mar 8-Sep"
## [253] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 10-Sep"
## [254] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 2 10-Sep 6-Mar"
## [255] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 3 3-Mar 5-Mar 6-Sep"
## [256] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 3 8-Sep 10-Sep 6-Mar"
## [257] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 8-Sep"
## [258] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 2 3-Mar 8-Sep"
## [259] "PMC12781783 zip/Table_S9_top1000_PI3KIC50.xlsx Hsapiens 1 3-Mar"
## [260] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 3-Mar"
## [261] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 3-Mar 10-Sep"
## [262] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 3-Mar"
## [263] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 6-Sep 3-Mar"
## [264] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 3-Mar 6-Sep"
## [265] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 6-Mar 6-Sep"
## [266] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 10-Sep 3-Mar"
## [267] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 3-Mar"
## [268] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 6-Mar"
## [269] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 3 3-Mar 6-Sep 7-Sep"
## [270] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 6-Sep 7-Mar"
## [271] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 6-Sep"
## [272] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 1-Mar 6-Sep"
## [273] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 10-Sep 3-Mar"
## [274] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 10-Sep"
## [275] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 3-Mar 10-Sep"
## [276] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 10-Sep"
## [277] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 10-Sep 6-Mar"
## [278] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 3-Mar 6-Sep"
## [279] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 3 3-Mar 5-Mar 6-Sep"
## [280] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 8-Sep 10-Sep"
## [281] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 3-Mar"
## [282] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 3-Mar 6-Sep"
## [283] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 3-Mar"
## [284] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 2 3-Mar 8-Sep"
## [285] "PMC12781783 zip/Table_S7_top1000_ERKIC50.xlsx Hsapiens 1 3-Mar"
## [286] "PMC12778141 PMC_DL/PMC12778141/supplementaryfiles/medi-105-e45033-s001.xlsx Hsapiens 1 45717"
## [287] "PMC12778141 PMC_DL/PMC12778141/supplementaryfiles/medi-105-e45033-s001.xlsx Hsapiens 12 45717 45721 45719 45722 45992 45723 45725 45720 45718 45724 45727 45726"
## [288] "PMC12774651 zip/Supplementary_Tables.xlsx Athaliana 4 45903 45750 45876 45875"
## [289] "PMC12775020 PMC_DL/PMC12775020/supplementaryfiles/41598_2025_29970_MOESM3_ESM.xlsx Mmusculus 1 38596"
## [290] "PMC12477835 zip/Supplementary_Table_8.xlsx Celegans 8 45748 45931 45932 45901 45719 45718 45809 45722"
## [291] "PMC12769960 PMC_DL/PMC12769960/supplementaryfiles/10238_2025_2026_MOESM2_ESM.xlsx Hsapiens 2 45717 45726"
## [292] "PMC12773779 PMC_DL/PMC12773779/supplementaryfiles/pnas.2509904122.sd07.xlsx Athaliana 1 37591"
## [293] "PMC12773779 PMC_DL/PMC12773779/supplementaryfiles/pnas.2509904122.sd03.xlsx Athaliana 14 38991 37895 37865 37469 39295 37165 38626 37500 38200 38930 37591 37135 37956 36982"
## [294] "PMC12773779 PMC_DL/PMC12773779/supplementaryfiles/pnas.2509904122.sd02.xlsx Athaliana 22 38991 37895 37865 37469 37834 37104 39295 37165 37530 38626 38231 37500 38200 38930 37500 37591 37135 37956 37135 39661 40391 36982"
## [295] "PMC12770561 PMC_DL/PMC12770561/supplementaryfiles/41467_2025_66632_MOESM10_ESM.xlsx Hsapiens 3 45176 45176 45180"
## [296] "PMC12769673 PMC_DL/PMC12769673/supplementaryfiles/41467_2025_66656_MOESM4_ESM.xlsx Hsapiens 1 14977"
## [297] "PMC12769673 PMC_DL/PMC12769673/supplementaryfiles/41467_2025_66656_MOESM4_ESM.xlsx Hsapiens 1 14977"
## [298] "PMC12769673 PMC_DL/PMC12769673/supplementaryfiles/41467_2025_66656_MOESM4_ESM.xlsx Hsapiens 1 14977"
## [299] "PMC12769673 PMC_DL/PMC12769673/supplementaryfiles/41467_2025_66656_MOESM4_ESM.xlsx Hsapiens 1 14977"
## [300] "PMC12769673 PMC_DL/PMC12769673/supplementaryfiles/41467_2025_66656_MOESM4_ESM.xlsx Hsapiens 1 14977"
## [301] "PMC12769673 PMC_DL/PMC12769673/supplementaryfiles/41467_2025_66656_MOESM4_ESM.xlsx Hsapiens 1 14977"
## [302] "PMC12769673 PMC_DL/PMC12769673/supplementaryfiles/41467_2025_66656_MOESM4_ESM.xlsx Hsapiens 1 14977"
## [303] "PMC12771847 PMC_DL/PMC12771847/supplementaryfiles/12864_2025_12252_MOESM8_ESM.xlsx Hsapiens 4 8-Mar 2-Mar 1-Mar 10-Mar"
## [304] "PMC12771847 PMC_DL/PMC12771847/supplementaryfiles/12864_2025_12252_MOESM8_ESM.xlsx Hsapiens 5 2-Mar 8-Mar 4-Sep 10-Mar 4-Sep"
## [305] "PMC12771377 zip/Table_S2.xlsx Ggallus 2 EN1-MARCO EN1-MARCO"
## [306] "PMC12768487 PMC_DL/PMC12768487/supplementaryfiles/NIHMS2129409-supplement-2.xlsx Hsapiens 20 45911 45721 45720 45909 45726 45718 45723 45724 45902 45717 45908 45717 45910 45722 45906 45907 45718 45719 45903 45725"
## [307] "PMC12768487 PMC_DL/PMC12768487/supplementaryfiles/NIHMS2129409-supplement-2.xlsx Hsapiens 20 45908 45725 45724 45906 45909 45910 45911 45720 45718 45726 45717 45721 45723 45718 45902 45722 45903 45901 45907 45717"
## [308] "PMC12768487 PMC_DL/PMC12768487/supplementaryfiles/NIHMS2129409-supplement-2.xlsx Hsapiens 20 45722 45911 45718 45720 45724 45717 45903 45910 45717 45909 45907 45902 45721 45723 45906 45908 45718 45725 45719 45726"
## [309] "PMC12768487 PMC_DL/PMC12768487/supplementaryfiles/NIHMS2129409-supplement-2.xlsx Hsapiens 20 45724 45901 45717 45903 45718 45721 45906 45722 45717 45726 45725 45910 45723 45907 45718 45902 45908 45909 45911 45720"
## [310] "PMC12766917 PMC_DL/PMC12766917/supplementaryfiles/table_s4_tcre_information_ziaf178.xlsx Hsapiens 21 45359 45356 45356 45360 45360 45353 45353 45353 45353 45358 45358 45358 45358 45352 45352 45352 45357 45357 45357 45357 45354"
## [311] "PMC12767815 PMC_DL/PMC12767815/supplementaryfiles/mmc1.xlsx Hsapiens 1 45353"
## [312] "PMC12767815 PMC_DL/PMC12767815/supplementaryfiles/mmc1.xlsx Hsapiens 1 45353"
## [313] "PMC12766398 zip/Supplementary_table_2.xlsx Hsapiens 1 45261"
## [314] "PMC12766398 zip/Supplementary_table_2.xlsx Hsapiens 1 45261"
## [315] "PMC12765388 PMC_DL/PMC12765388/supplementaryfiles/mmc5.xlsx Hsapiens 1 37865"
## [316] "PMC12765388 PMC_DL/PMC12765388/supplementaryfiles/mmc6.xlsx Hsapiens 1 37316"
## [317] "PMC12757036 zip/adw7768_tables_s1_to_s26.xlsx Hsapiens 1 45358"
## [318] "PMC12757036 zip/adw7768_tables_s1_to_s26.xlsx Hsapiens 23 45992 45908 45726 45904 45720 45901 45718 45903 45722 45725 45721 45717 45910 45909 45717 45723 45902 45724 45911 45907 45906 45718 45719"
## [319] "PMC12757029 zip/Supplementary_Tables.xlsx Hsapiens 27 45360 45360 45550 45360 45360 45354 45354 45354 45354 45542 45542 45542 45360 45360 45360 45360 45357 45360 45360 45354 45354 45354 45354 45354 45542 45542 45542"
## [320] "PMC12757029 zip/Supplementary_Tables.xlsx Hsapiens 5 45360 45354 45542 45550 45357"
## [321] "PMC12757029 zip/Supplementary_Tables.xlsx Hsapiens 47 45353 45359 45359 45359 45359 45356 45356 45356 45356 45360 45358 45358 45355 45355 45355 45355 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45352 45357 45357 45362 45362 45362 45362 45354 45354 45354 45627 45627 45627 45627"
## [322] "PMC12757029 zip/Supplementary_Tables.xlsx Hsapiens 23 45356 45360 45360 45360 45360 45357 45357 45357 45542 45550 45550 45356 45356 45360 45360 45354 45354 45354 45354 45354 45542 45542 45542"
## [323] "PMC12753682 PMC_DL/PMC12753682/supplementaryfiles/41423_2025_1369_MOESM8_ESM.xlsx Hsapiens 13 37865 38231 39326 38961 40787 41153 41883 39692 37500 40057 38596 40422 37316"
## [324] "PMC12753682 PMC_DL/PMC12753682/supplementaryfiles/41423_2025_1369_MOESM8_ESM.xlsx Hsapiens 13 39692 40787 38596 38961 37500 37865 38231 40057 37316 39326 40422 41153 41883"
## [325] "PMC12753682 PMC_DL/PMC12753682/supplementaryfiles/41423_2025_1369_MOESM8_ESM.xlsx Hsapiens 13 37865 38231 39326 38961 40787 41153 41883 39692 37500 40057 38596 40422 37316"
## [326] "PMC12753682 PMC_DL/PMC12753682/supplementaryfiles/41423_2025_1369_MOESM8_ESM.xlsx Hsapiens 13 38961 37500 39326 39692 40787 41883 37865 38231 37316 40057 40422 41153 38596"
## [327] "PMC12753682 PMC_DL/PMC12753682/supplementaryfiles/41423_2025_1369_MOESM8_ESM.xlsx Hsapiens 13 37865 38231 39326 38961 40787 41153 41883 39692 37500 40057 38596 40422 37316"
## [328] "PMC12753682 PMC_DL/PMC12753682/supplementaryfiles/41423_2025_1369_MOESM8_ESM.xlsx Hsapiens 13 40787 37865 37500 37316 38961 39326 40057 38231 40422 39692 41153 41883 38596"
## [329] "PMC12753682 PMC_DL/PMC12753682/supplementaryfiles/41423_2025_1369_MOESM8_ESM.xlsx Hsapiens 10 37865 38231 39326 38961 40787 39692 37500 40057 40422 37316"
## [330] "PMC12753682 PMC_DL/PMC12753682/supplementaryfiles/41423_2025_1369_MOESM8_ESM.xlsx Hsapiens 10 39692 40422 38961 37865 37316 39326 37500 40057 40787 38231"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 Celegans Dmelanogaster Drerio Ggallus
## 5 1 8 7 5
## Hsapiens Mmusculus Rnorvegicus Scerevisiae
## 277 24 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##
## PMC12477835 PMC12753682 PMC12757029 PMC12757036 PMC12765388 PMC12766398
## 1 8 4 2 2 2
## PMC12766917 PMC12767815 PMC12768487 PMC12769673 PMC12769960 PMC12770561
## 1 2 4 7 1 1
## PMC12771377 PMC12771847 PMC12773779 PMC12774651 PMC12775020 PMC12778141
## 1 2 3 1 1 2
## PMC12781783 PMC12783525 PMC12784965 PMC12789528 PMC12793829 PMC12796321
## 92 1 4 1 1 1
## PMC12796744 PMC12797063 PMC12797436 PMC12800067 PMC12800293 PMC12801463
## 3 1 6 1 2 1
## PMC12801672 PMC12802902 PMC12804938 PMC12807715 PMC12808549 PMC12808955
## 1 1 3 1 1 5
## PMC12808957 PMC12810618 PMC12810641 PMC12810902 PMC12811338 PMC12813248
## 1 2 7 11 1 3
## PMC12814444 PMC12815961 PMC12817070 PMC12818872 PMC12819152 PMC12819415
## 3 1 3 1 2 1
## PMC12819441 PMC12820099 PMC12820176 PMC12821805 PMC12821903 PMC12822184
## 13 1 1 1 1 2
## PMC12822518 PMC12823390 PMC12824155 PMC12824659 PMC12824682 PMC12826143
## 8 3 2 20 1 1
## PMC12827549 PMC12830518 PMC12830819 PMC12832762 PMC12832931 PMC12833344
## 2 1 7 1 3 2
## PMC12835543 PMC12837101 PMC12839865 PMC12841099 PMC12841453 PMC12842411
## 6 16 1 1 6 1
## PMC12844564 PMC12846996 PMC12847017 PMC12852518 PMC12853625 PMC12854938
## 1 1 1 1 1 1
## PMC12856215 PMC12857072 PMC7618654
## 10 1 5summary(as.numeric(DIST))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.000 1.000 1.000 4.074 3.000 92.000hist(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
## 19 PMC12781783 92
## 58 PMC12824659 20
## 68 PMC12837101 16
## 49 PMC12819441 13
## 40 PMC12810902 11
## 79 PMC12856215 10
## 2 PMC12753682 8
## 55 PMC12822518 8
## 10 PMC12769673 7
## 39 PMC12810641 7
## 63 PMC12830819 7
## 27 PMC12797436 6
## 67 PMC12835543 6
## 71 PMC12841453 6
## 36 PMC12808955 5
## 81 PMC7618654 5
## 3 PMC12757029 4
## 9 PMC12768487 4
## 21 PMC12784965 4
## 15 PMC12773779 3MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES## [1] "PMC12781783"# 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## PMC12477835 PMC12753682 PMC12757029 PMC12757036 PMC12765388 PMC12766398
## 8 98 102 24 2 2
## PMC12766917 PMC12767815 PMC12768487 PMC12769673 PMC12769960 PMC12770561
## 21 2 80 7 2 3
## PMC12771377 PMC12771847 PMC12773779 PMC12774651 PMC12775020 PMC12778141
## 2 9 37 4 1 13
## PMC12781783 PMC12783525 PMC12784965 PMC12789528 PMC12793829 PMC12796321
## 156 28 50 28 14 1
## PMC12796744 PMC12797063 PMC12797436 PMC12800067 PMC12800293 PMC12801463
## 6 12 10 27 36 34
## PMC12801672 PMC12802902 PMC12804938 PMC12807715 PMC12808549 PMC12808955
## 22 4 72 3 1 14
## PMC12808957 PMC12810618 PMC12810641 PMC12810902 PMC12811338 PMC12813248
## 2 108 17 192 3 57
## PMC12814444 PMC12815961 PMC12817070 PMC12818872 PMC12819152 PMC12819415
## 5 1 90 2 9 3
## PMC12819441 PMC12820099 PMC12820176 PMC12821805 PMC12821903 PMC12822184
## 44 1 103 1 2 48
## PMC12822518 PMC12823390 PMC12824155 PMC12824659 PMC12824682 PMC12826143
## 291 5 56 24 8 25
## PMC12827549 PMC12830518 PMC12830819 PMC12832762 PMC12832931 PMC12833344
## 13 1 140 1 75 5
## PMC12835543 PMC12837101 PMC12839865 PMC12841099 PMC12841453 PMC12842411
## 35 51 1 23 64 12
## PMC12844564 PMC12846996 PMC12847017 PMC12852518 PMC12853625 PMC12854938
## 1 1 2 14 12 3
## PMC12856215 PMC12857072 PMC7618654
## 1011 1 33hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
head(NERR_DF,20)## NERR
## PMC12856215 1011
## PMC12822518 291
## PMC12810902 192
## PMC12781783 156
## PMC12830819 140
## PMC12810618 108
## PMC12820176 103
## PMC12757029 102
## PMC12753682 98
## PMC12817070 90
## PMC12768487 80
## PMC12832931 75
## PMC12804938 72
## PMC12841453 64
## PMC12813248 57
## PMC12824155 56
## PMC12837101 51
## PMC12784965 50
## PMC12822184 48
## PMC12819441 44MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR## [1] "PMC12856215"Journals affected
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
### JSON PARSING is more reliable than XML
ARTICLES <- esummary( GENELIST_ERROR_ARTICLES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA$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] 54par(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] "12781783"
##
## $result$`12781783`
## $result$`12781783`$uid
## [1] "12781783"
##
## $result$`12781783`$pubdate
## [1] "2025 Dec 3"
##
## $result$`12781783`$epubdate
## [1] "2025 Dec 3"
##
## $result$`12781783`$printpubdate
## [1] ""
##
## $result$`12781783`$source
## [1] "BMC Biol"
##
## $result$`12781783`$authors
## name authtype
## 1 Wang K Author
## 2 Li B Author
## 3 Xu M Author
## 4 Ding D Author
## 5 Zheng Q Author
## 6 Tian G Author
## 7 Zeng X Author
## 8 Yang J Author
##
## $result$`12781783`$title
## [1] "MCLRP: enhanced prediction of anticancer drug response through low-rank matrix completion and transcriptomic profiling."
##
## $result$`12781783`$volume
## [1] "24"
##
## $result$`12781783`$issue
## [1] "1"
##
## $result$`12781783`$pages
## [1] "4"
##
## $result$`12781783`$articleids
## idtype value
## 1 pmid 41340127
## 2 pmcid PMC12781783
## 3 doi 10.1186/s12915-025-02457-8
## 4 pii 10.1186/s12915-025-02457-8
##
## $result$`12781783`$fulljournalname
## [1] "BMC biology"
##
## $result$`12781783`$sortdate
## [1] "2025/12/03 00:00"
##
## $result$`12781783`$pmclivedate
## [1] "2026/01/09"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] "12856215"
##
## $result$`12856215`
## $result$`12856215`$uid
## [1] "12856215"
##
## $result$`12856215`$pubdate
## [1] "2026 Jan 22"
##
## $result$`12856215`$epubdate
## [1] ""
##
## $result$`12856215`$printpubdate
## [1] "2026 Jan 22"
##
## $result$`12856215`$source
## [1] "Nucleic Acids Res"
##
## $result$`12856215`$authors
## name authtype
## 1 Carr SM Author
## 2 Liu G Author
## 3 Barczak W Author
## 4 Syffudin H Author
## 5 Munro S Author
## 6 Reyna-Jeldes D Author
## 7 Vendrell I Author
## 8 Kessler B Author
## 9 Cribbs AP Author
## 10 Kanapin A Author
## 11 Samsonova A Author
## 12 La Thangue NB Author
##
## $result$`12856215`$title
## [1] "Separate transcription and splicing gene networks are linked and coordinated by the pRb-E2F pathway."
##
## $result$`12856215`$volume
## [1] "54"
##
## $result$`12856215`$issue
## [1] "3"
##
## $result$`12856215`$pages
## [1] ""
##
## $result$`12856215`$articleids
## idtype value
## 1 pmid 41614303
## 2 pmcid PMC12856215
## 3 doi 10.1093/nar/gkag016
## 4 pii 8445238
##
## $result$`12856215`$fulljournalname
## [1] "Nucleic acids research"
##
## $result$`12856215`$sortdate
## [1] "2026/01/22 00:00"
##
## $result$`12856215`$pmclivedate
## [1] "2026/01/31"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