Gene Name Error Monthly Dashboard
Mark Ziemann
2026-07-18
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="2024/6"
#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 4000pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 3731writeLines(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] 4479NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 850GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 545NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 285ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 172GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC11212735" "PMC11209080" "PMC11209011" "PMC11210073" "PMC11208570"
## [6] "PMC11200816" "PMC10769850" "PMC11197386" "PMC11196711" "PMC11194900"
## [11] "PMC11195603" "PMC11193738" "PMC11192824" "PMC11190585" "PMC11190204"
## [16] "PMC11189927" "PMC11186912" "PMC11187386" "PMC11187367" "PMC11186173"
## [21] "PMC11186636" "PMC11186088" "PMC10756262" "PMC11180607" "PMC11181613"
## [26] "PMC11180117" "PMC11178499" "PMC11176086" "PMC11172763" "PMC11171932"
## [31] "PMC11171046" "PMC11176395" "PMC11169032" "PMC11170780" "PMC11167437"
## [36] "PMC11165217" "PMC11165782" "PMC11163233" "PMC11162987" "PMC11162794"
## [41] "PMC11157162" "PMC11161060" "PMC11153616" "PMC11153834" "PMC11153731"
## [46] "PMC11152081" "PMC11150558" "PMC11151630" "PMC11148644" "PMC11148773"
## [51] "PMC11148058" "PMC11148184" "PMC11148543" "PMC11148542" "PMC11149427"
## [56] "PMC11148150" "PMC11146594" "PMC11145889" "PMC11145787" "PMC11141942"
## [61] "PMC10760529"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 61ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.2140351Look 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] "PMC11212735 zip/adf3411_table_s6.xlsx Hsapiens 14 44080 44080 44075 44075 44075 43892 43892 44075 44075 44075 44075 44079 44080 43892"
## [2] "PMC11209080 zip/Table_S6.xlsx Hsapiens 29 45353 45538 45539 45353 45542 45541 45358 45546 45360 45547 45355 45352 45357 45549 45543 45359 45537 45627 45361 45354 45536 45550 45362 45544 45540 45352 45545 45356 45536"
## [3] "PMC11209080 zip/Table_S5.xlsx Hsapiens 2 45540 45546"
## [4] "PMC11209080 zip/Table_S2.xlsx Hsapiens 29 45353 45538 45539 45353 45542 45541 45358 45546 45360 45547 45355 45352 45357 45549 45543 45359 45537 45627 45361 45354 45536 45550 45362 45544 45540 45352 45545 45356 45536"
## [5] "PMC11209080 zip/Table_S2.xlsx Hsapiens 2 45540 45546"
## [6] "PMC11209080 zip/Table_S2.xlsx Hsapiens 1 45546"
## [7] "PMC11209011 PMC_DL/PMC11209011/supplementaryfiles/mmc2.xlsx Hsapiens 16 37135 37226 38961 37012 37500 37865 38108 38231 38596 39326 39692 40057 40422 40787 41153 41883"
## [8] "PMC11210073 PMC_DL/PMC11210073/supplementaryfiles/additional_files_bbae306.xlsx Hsapiens 24 45550 45545 45358 45355 45537 45546 45357 45362 45354 45543 45542 45549 45627 45359 45356 45360 45547 45536 45539 45361 45544 45540 45538 45541"
## [9] "PMC11208570 PMC_DL/PMC11208570/supplementaryfiles/41598_2024_65769_MOESM3_ESM.xlsx Hsapiens 4 43354 43350 43345 43352"
## [10] "PMC11200816 PMC_DL/PMC11200816/supplementaryfiles/13048_2024_1463_MOESM1_ESM.xlsx Hsapiens 1 45627"
## [11] "PMC10769850 PMC_DL/PMC10769850/supplementaryfiles/pnas.2315865120.sd01.xlsx Hsapiens 1 44896"
## [12] "PMC10769850 PMC_DL/PMC10769850/supplementaryfiles/pnas.2315865120.sd01.xlsx Hsapiens 1 44896"
## [13] "PMC11197386 PMC_DL/PMC11197386/supplementaryfiles/Table2.XLSX Hsapiens 1 45543"
## [14] "PMC11196711 PMC_DL/PMC11196711/supplementaryfiles/41598_2024_65327_MOESM8_ESM.xlsx Hsapiens 28 44443 44258 44453 44445 44257 44441 44265 44261 44444 44266 44260 44256 44257 44447 44262 44531 44442 44449 44259 44454 44256 44263 44440 44264 44448 44450 44451 44446"
## [15] "PMC11194900 PMC_DL/PMC11194900/supplementaryfiles/12891_2024_7589_MOESM1_ESM.xlsx Hsapiens 25 45352 45357 45359 45540 45352 45550 45356 45541 45536 45542 45538 45360 45544 45545 45358 45546 45543 45354 45549 45353 45353 45361 45537 45355 45539"
## [16] "PMC11194900 PMC_DL/PMC11194900/supplementaryfiles/12891_2024_7589_MOESM3_ESM.xlsx Hsapiens 26 44819 44806 44811 44813 44805 44626 44622 44810 44627 44625 44629 44815 44621 44814 44808 44628 44805 44812 44809 44623 44622 44807 44621 44816 44630 44896"
## [17] "PMC11195603 PMC_DL/PMC11195603/supplementaryfiles/jamapsychiatry-e241429-s002.xlsx Hsapiens 6 45172 45173 44987 45178 44986 44986"
## [18] "PMC11195603 PMC_DL/PMC11195603/supplementaryfiles/jamapsychiatry-e241429-s002.xlsx Hsapiens 13 44993 44987 44987 44986 45180 45179 45176 45171 44994 45172 44995 44988 45178"
## [19] "PMC11195603 PMC_DL/PMC11195603/supplementaryfiles/jamapsychiatry-e241429-s002.xlsx Hsapiens 2 44622 44806"
## [20] "PMC11195603 PMC_DL/PMC11195603/supplementaryfiles/jamapsychiatry-e241429-s002.xlsx Hsapiens 5 44622 44814 44806 44621 44623"
## [21] "PMC11195603 PMC_DL/PMC11195603/supplementaryfiles/jamapsychiatry-e241429-s002.xlsx Hsapiens 2 44806 44622"
## [22] "PMC11195603 PMC_DL/PMC11195603/supplementaryfiles/jamapsychiatry-e241429-s002.xlsx Hsapiens 2 44806 44622"
## [23] "PMC11195603 PMC_DL/PMC11195603/supplementaryfiles/jamapsychiatry-e241429-s002.xlsx Hsapiens 2 44987 45171"
## [24] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM11_ESM.xlsx Hsapiens 1 40057"
## [25] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM5_ESM.xlsx Hsapiens 1 37681"
## [26] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM5_ESM.xlsx Hsapiens 5 40057 40057 37500 37681 37316"
## [27] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM8_ESM.xlsx Hsapiens 2 40422 40057"
## [28] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM8_ESM.xlsx Hsapiens 2 40057 40422"
## [29] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM8_ESM.xlsx Hsapiens 1 40057"
## [30] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM4_ESM.xlsx Hsapiens 1 37681"
## [31] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM4_ESM.xlsx Hsapiens 25 40603 37226 37226 36951 40787 40057 37681 37681 39508 38231 40057 36951 40057 39692 36951 40057 40787 40057 40603 40422 37226 42248 37226 42248 37226"
## [32] "PMC11193738 PMC_DL/PMC11193738/supplementaryfiles/41467_2024_48647_MOESM4_ESM.xlsx Hsapiens 13 40057 40057 37316 40057 40057 39692 40057 40057 40057 39508 37316 39508 40422"
## [33] "PMC11192824 PMC_DL/PMC11192824/supplementaryfiles/10238_2024_1389_MOESM8_ESM.xlsx Hsapiens 6 39326 39142 36951 40238 40057 36951"
## [34] "PMC11190585 PMC_DL/PMC11190585/supplementaryfiles/CNR2-7-e2107-s007.xlsx Hsapiens 7 45566 45566 45567 45566 45566 45566 45566"
## [35] "PMC11190204 PMC_DL/PMC11190204/supplementaryfiles/42003_2024_6421_MOESM3_ESM.xlsx Mmusculus 12 45172 44986 44986 45180 45178 44987 45177 44994 45175 45179 44992 44988"
## [36] "PMC11189927 PMC_DL/PMC11189927/supplementaryfiles/41467_2024_49450_MOESM7_ESM.xlsx Mmusculus 21 44628 44810 44623 44805 44812 44813 44811 44815 44622 44629 44806 44808 44814 44809 44622 44627 44626 44625 44624 44621 44816"
## [37] "PMC11189927 PMC_DL/PMC11189927/supplementaryfiles/41467_2024_49450_MOESM7_ESM.xlsx Mmusculus 1 44623"
## [38] "PMC11189927 PMC_DL/PMC11189927/supplementaryfiles/41467_2024_49450_MOESM7_ESM.xlsx Mmusculus 22 44628 44806 44808 44815 44627 44811 44629 44622 44622 44805 44809 44810 44626 44624 44625 44813 44623 44812 44814 44631 44816 44621"
## [39] "PMC11189927 PMC_DL/PMC11189927/supplementaryfiles/41467_2024_49450_MOESM7_ESM.xlsx Mmusculus 1 44808"
## [40] "PMC11186912 PMC_DL/PMC11186912/supplementaryfiles/253_2024_13223_MOESM1_ESM.xlsx Mmusculus 6 37500 40787 38961 39326 39692 38596"
## [41] "PMC11187386 PMC_DL/PMC11187386/supplementaryfiles/gutjnl-2023-330414supp002.xlsx Mmusculus 1 45174"
## [42] "PMC11187367 zip/Supplementary_Table_14-DE_genes_between_2_bulk_subgroups_for_the_bulk_RNA-seq_data_with_20_OA_patients,_the_Group_A_and_the_Group_B.xlsx Hsapiens 3 45536 45353 45544"
## [43] "PMC11187367 zip/Supplementary_Table_14-DE_genes_between_2_bulk_subgroups_for_the_bulk_RNA-seq_data_with_20_OA_patients,_the_Group_A_and_the_Group_B.xlsx Hsapiens 2 45359 45537"
## [44] "PMC11186173 PMC_DL/PMC11186173/supplementaryfiles/12859_2024_5835_MOESM3_ESM.xlsx Hsapiens 1 44257"
## [45] "PMC11186636 PMC_DL/PMC11186636/supplementaryfiles/elife-91611-fig1-data1.xlsx Hsapiens 26 44621 44621 44624 44810 44630 44807 44815 44808 44806 44813 44629 44627 44623 44628 44631 44816 44812 44622 44622 44809 44805 44626 44818 44625 44896 44814"
## [46] "PMC11186636 PMC_DL/PMC11186636/supplementaryfiles/elife-91611-fig4-data1.xlsx Hsapiens 8 9-Mar 1-Mar 7-Mar 2-Mar 6-Mar 3-Mar 5-Mar 8-Mar"
## [47] "PMC11186636 PMC_DL/PMC11186636/supplementaryfiles/elife-91611-fig4-data1.xlsx Hsapiens 8 9-Mar 2-Mar 1-Mar 7-Mar 6-Mar 3-Mar 5-Mar 8-Mar"
## [48] "PMC11186088 PMC_DL/PMC11186088/supplementaryfiles/12935_2024_3403_MOESM10_ESM.xls Hsapiens 3 44987 45176 44992"
## [49] "PMC11186088 PMC_DL/PMC11186088/supplementaryfiles/12935_2024_3403_MOESM9_ESM.xls Hsapiens 26 45261 44995 44996 44986 44987 44988 44989 44990 44991 44992 44993 44994 45184 45179 45180 45181 45183 45170 45171 45172 45173 45174 45175 45176 45177 45178"
## [50] "PMC10756262 PMC_DL/PMC10756262/supplementaryfiles/pnas.2310670120.sd02.xlsx Athaliana 13 45205 45205 45018 45018 45204 45171 45140 45140 45203 45203 45170 45170 45144"
## [51] "PMC10756262 PMC_DL/PMC10756262/supplementaryfiles/pnas.2310670120.sd02.xlsx Athaliana 20 45205 45172 45172 45172 45018 45018 45018 45204 45173 45171 45140 45140 45171 45203 45017 45019 45170 45170 45143 45144"
## [52] "PMC10756262 PMC_DL/PMC10756262/supplementaryfiles/pnas.2310670120.sd02.xlsx Athaliana 11 45172 45018 45018 45018 45204 45173 45171 45140 45203 45170 45143"
## [53] "PMC10756262 PMC_DL/PMC10756262/supplementaryfiles/pnas.2310670120.sd02.xlsx Athaliana 12 45172 45018 45018 45018 45204 45173 45171 45140 45017 45170 45143 45144"
## [54] "PMC10756262 PMC_DL/PMC10756262/supplementaryfiles/pnas.2310670120.sd02.xlsx Athaliana 1 45205"
## [55] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM8_ESM.xlsx Mmusculus 5 44990 45180 44987 45176 45171"
## [56] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM8_ESM.xlsx Mmusculus 8 44990 45180 44987 45176 45171 45180 44990 45178"
## [57] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM8_ESM.xlsx Mmusculus 3 44987 45176 45171"
## [58] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM8_ESM.xlsx Rnorvegicus 4 44987 45176 45171 45178"
## [59] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM9_ESM.xlsx Mmusculus 47 44806 44806 44806 44624 44624 44621 44621 44622 44622 44622 44622 44627 44815 44815 44815 44818 44818 44628 44805 44805 44621 44811 44811 44811 44811 44812 44812 44812 44808 44813 44813 44813 44813 44813 44630 44630 44631 44631 44626 44626 44626 44816 44809 44809 44809 44622 44810"
## [60] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM5_ESM.xlsx Mmusculus 2 44805 44807"
## [61] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM5_ESM.xlsx Mmusculus 2 44805 44621"
## [62] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM5_ESM.xlsx Mmusculus 2 44805 44621"
## [63] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM5_ESM.xlsx Mmusculus 1 44807"
## [64] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM5_ESM.xlsx Mmusculus 3 44809 44807 44621"
## [65] "PMC11180607 PMC_DL/PMC11180607/supplementaryfiles/41587_2023_1931_MOESM5_ESM.xlsx Mmusculus 1 44805"
## [66] "PMC11181613 PMC_DL/PMC11181613/supplementaryfiles/12864_2024_10464_MOESM5_ESM.xlsx Hsapiens 3 44989 44989 44992"
## [67] "PMC11180117 PMC_DL/PMC11180117/supplementaryfiles/41467_2024_49571_MOESM5_ESM.xlsx Athaliana 11 44805 44653 44652 44654 44838 44806 44807 44840 44835 44835 44805"
## [68] "PMC11180117 PMC_DL/PMC11180117/supplementaryfiles/41467_2024_49571_MOESM5_ESM.xlsx Athaliana 8 44835 44805 44807 44653 44836 44839 44835 44840"
## [69] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM8_ESM.xlsx Mmusculus 17 45175 45170 44987 45178 44993 44991 45176 45180 44992 45177 44990 44988 44987 44986 45173 45179 45174"
## [70] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM6_ESM.xlsx Mmusculus 1 44447"
## [71] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM6_ESM.xlsx Mmusculus 1 44812"
## [72] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM12_ESM.xlsx Mmusculus 4 44447 44449 44263 44444"
## [73] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM5_ESM.xlsx Mmusculus 17 45176 45178 45179 45173 44993 44986 45175 44988 44987 44992 45170 45177 44991 44987 45180 45174 44990"
## [74] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM14_ESM.xlsx Mmusculus 1 44447"
## [75] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM14_ESM.xlsx Mmusculus 1 44812"
## [76] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM14_ESM.xlsx Mmusculus 1 44621"
## [77] "PMC11178499 PMC_DL/PMC11178499/supplementaryfiles/41556_2024_1424_MOESM7_ESM.xlsx Mmusculus 17 45174 45178 45173 45170 44987 45180 44988 45176 44990 44993 44991 45175 45179 44992 45177 44987 44986"
## [78] "PMC11176086 PMC_DL/PMC11176086/supplementaryfiles/41588_2024_1763_MOESM4_ESM.xlsx Hsapiens 2 44257 44256"
## [79] "PMC11172763 zip/ijms-2993601-supplementary.xlsx Hsapiens 1 45539"
## [80] "PMC11171932 zip/Table_S5._All_differentially_expressed_genes_annotated_SN14_and_R122.xlsx Athaliana 3 44440 44441 4-Oct,AtOCT4"
## [81] "PMC11171046 zip/1.Supplementary_File_S1.xlsx Hsapiens 19 42796 42993 42803 42982 42987 42979 42797 42983 42984 42795 42989 42980 42800 42802 42799 42801 42988 42986 42985"
## [82] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 34 44989 45180 45173 45177 45172 45178 44989 45175 45174 44994 45173 44993 45176 44996 45178 44987 45170 45171 44993 44988 44987 44991 44992 45176 44986 45178 44995 44996 44994 45170 44986 44993 44987 45178"
## [83] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 38 44079 43894 44085 44081 44079 44082 44077 44083 43894 43899 44078 43898 44081 44083 43897 44080 43901 44075 44078 43892 43896 44085 43892 43898 43897 44081 43891 44076 43901 43900 44080 44083 43893 44075 43891 43898 43892 44083"
## [84] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 34 43894 44081 44081 44085 44078 44083 44077 44082 43899 43894 44078 44079 44078 44081 44081 43893 43892 43892 43898 44076 43891 44085 43896 44075 43897 44083 43900 43901 44080 44075 43891 43892 44083 43898"
## [85] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 29 45174 45174 44992 44993 44987 45176 45172 45178 44991 45174 44989 45173 44994 45176 44991 45177 45174 44987 44988 45177 45173 44986 45178 45170 44996 45175 44995 45172 45170"
## [86] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 29 44079 44081 43896 43897 44078 44083 43894 43901 43896 44079 44082 44079 44077 43899 44078 43893 44085 43892 43898 43892 44075 43900 44083 44082 43891 44080 44077 43899 44075"
## [87] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 9 43160 43160 43160 43170 43163 43349 43161 43169 43352"
## [88] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 6 43346 43167 43353 43353 43160 43163"
## [89] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 10 44076 43891 43891 43901 44083 43893 44084 43901 43900 44082"
## [90] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 10 44080 43891 43893 44085 43891 44082 43893 44081 43898 44080"
## [91] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 9 43160 43160 43160 43170 43169 43163 43161 43352 43349"
## [92] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 25 45172 45177 45174 44992 44994 45171 45176 44987 44990 45179 45180 45173 44988 44993 45170 44989 44986 45175 44991 45183 44996 45178 44987 44986 44995"
## [93] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 25 44987 45172 44988 44994 45173 45175 45171 45177 44986 45176 45179 44991 45180 44987 44996 44986 44992 45183 44995 44993 44989 45174 45178 44990 45170"
## [94] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 12 44989 45173 45177 44992 44992 45172 44986 45178 44990 44994 44995 44987"
## [95] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 2 44986 44986"
## [96] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Mmusculus 11 43162 43352 43346 43351 43352 43346 43160 43167 43163 43353 43353"
## [97] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Hsapiens 41 43897 44081 44083 44085 44081 43891 44076 44085 44075 44082 43892 43898 43896 43893 44077 44084 44080 44078 44082 44083 43893 44080 43891 44078 43894 43892 44083 43899 43898 44079 43893 44083 44077 44083 44078 44083 43894 44079 44083 44083 44079"
## [98] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Hsapiens 28 43897 43895 44076 43898 44081 44082 43893 43891 43893 44085 44075 44076 44077 44084 44082 43892 44083 43892 44085 44076 44080 43893 43896 44078 44083 44075 43891 44078"
## [99] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Hsapiens 43 43897 44081 44075 44083 44085 44082 43891 44085 43893 44084 44080 44078 43896 43898 43892 43892 44082 43898 43893 44083 44079 44083 43891 44078 43899 44077 44079 43900 44084 43894 44077 44080 43901 44078 43891 44083 44083 44078 43892 44075 44083 44082 44083"
## [100] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Hsapiens 1 44088"
## [101] "PMC11176395 PMC_DL/PMC11176395/supplementaryfiles/41467_2024_49336_MOESM4_ESM.xlsx Hsapiens 6 44991 44992 44986 44988 44993 44986"
## [102] "PMC11169032 PMC_DL/PMC11169032/supplementaryfiles/425_2024_4454_MOESM6_ESM.xlsx Athaliana 3 36982 38930 38200"
## [103] "PMC11170780 PMC_DL/PMC11170780/supplementaryfiles/40246_2024_625_MOESM1_ESM.xlsx Hsapiens 2 37834 37104"
## [104] "PMC11167437 PMC_DL/PMC11167437/supplementaryfiles/mmc5.xlsx Hsapiens 1 45178"
## [105] "PMC11165217 PMC_DL/PMC11165217/supplementaryfiles/DataSheet_2.xlsx Hsapiens 1 44986"
## [106] "PMC11165217 PMC_DL/PMC11165217/supplementaryfiles/DataSheet_2.xlsx Hsapiens 2 44986 44993"
## [107] "PMC11165217 PMC_DL/PMC11165217/supplementaryfiles/DataSheet_2.xlsx Hsapiens 2 44986 44993"
## [108] "PMC11165782 PMC_DL/PMC11165782/supplementaryfiles/40246_2024_627_MOESM6_ESM.xlsx Hsapiens 2 45179 44995"
## [109] "PMC11163233 zip/Supplementary_files/Supplementary_Table_S2_.xlsx Hsapiens 3 44078 44084 43891"
## [110] "PMC11162987 PMC_DL/PMC11162987/supplementaryfiles/12672_2024_1066_MOESM5_ESM.xlsx Hsapiens 3 44445 44264 44448"
## [111] "PMC11162794 zip/Table_S6.xlsx Hsapiens 7 44809 44806 44806 44806 44806 44806 44806"
## [112] "PMC11162794 zip/Table_S6.xlsx Hsapiens 4 45537 45537 45537 45537"
## [113] "PMC11162794 zip/Table_S2.xlsx Hsapiens 7 45171 44991 45178 44992 44991 44991 44991"
## [114] "PMC11162794 zip/Table_S2.xlsx Hsapiens 2 44986 44993"
## [115] "PMC11162794 zip/Table_S2.xlsx Dmelanogaster 1 45171"
## [116] "PMC11157162 PMC_DL/PMC11157162/supplementaryfiles/DAD2-16-e12597-s002.xlsx Hsapiens 1 45178"
## [117] "PMC11161060 PMC_DL/PMC11161060/supplementaryfiles/pbio.3002629.s010.xlsx Dmelanogaster 14 42252 42252 42249 42248 42339 42339 42339 42251 42251 42251 42251 42251 42251 42251"
## [118] "PMC11161060 PMC_DL/PMC11161060/supplementaryfiles/pbio.3002629.s009.xlsx Dmelanogaster 14 42339 42339 42339 42251 42251 42251 42251 42251 42251 42251 42252 42252 42249 42248"
## [119] "PMC11153616 PMC_DL/PMC11153616/supplementaryfiles/41431_2024_1573_MOESM3_ESM.xlsx Ggallus 2 45360 45360"
## [120] "PMC11153834 PMC_DL/PMC11153834/supplementaryfiles/goae057_supplementary_data.xlsx Hsapiens 4 44623 44631 44814 44626"
## [121] "PMC11153731 PMC_DL/PMC11153731/supplementaryfiles/Table_3.xlsx Hsapiens 1 44994"
## [122] "PMC11152081 zip/Supplementary_Table_4_G3-2024-404884.xlsx Scerevisiae 2 44470 44340"
## [123] "PMC11152081 zip/Supplementary_Table_4_G3-2024-404884.xlsx Scerevisiae 1 44340"
## [124] "PMC11152081 zip/Supplementary_Table_4_G3-2024-404884.xlsx Scerevisiae 1 45200"
## [125] "PMC11152081 zip/Supplementary_Table_5_G3-2024-404884.xlsx Scerevisiae 2 45200 45070"
## [126] "PMC11152081 zip/Supplementary_Table_5_G3-2024-404884.xlsx Dmelanogaster 2 45200 45070"
## [127] "PMC11150558 PMC_DL/PMC11150558/supplementaryfiles/Table_3.XLSX Mmusculus 35 44986 44995 44986 44986 44996 45176 44988 44986 44996 44986 44986 44986 44986 44986 44986 44986 44996 44996 44986 44986 45184 44986 44996 44986 45176 44986 44986 44986 44986 44986 44996 44987 44986 44986 45183"
## [128] "PMC11150558 PMC_DL/PMC11150558/supplementaryfiles/Table_3.XLSX Mmusculus 39 44986 44995 45176 44986 45174 44996 45183 44986 44996 44986 44986 44986 44986 44986 44986 44986 44986 44986 44986 44989 45176 44986 44986 44986 44986 44986 44996 44986 44986 44986 44986 45184 44986 44986 44987 44996 44986 44986 44988"
## [129] "PMC11150558 PMC_DL/PMC11150558/supplementaryfiles/Table_8.XLSX Mmusculus 1 45542"
## [130] "PMC11151630 PMC_DL/PMC11151630/supplementaryfiles/10194_2024_1802_MOESM1_ESM.xlsx Hsapiens 12 45352 45358 45355 45353 45360 45357 45359 45627 45361 45354 45362 45356"
## [131] "PMC11148644 PMC_DL/PMC11148644/supplementaryfiles/mmc12.xlsx Hsapiens 1 41883"
## [132] "PMC11148644 PMC_DL/PMC11148644/supplementaryfiles/mmc12.xlsx Hsapiens 3 41883 37012 37865"
## [133] "PMC11148773 PMC_DL/PMC11148773/supplementaryfiles/mmc10.xlsx Hsapiens 27 38231 39873 41883 40787 39326 37500 38961 40057 40422 40603 39508 37135 36951 39692 37681 40238 38596 41153 38047 38777 37316 37316 37226 36951 37865 38412 39142"
## [134] "PMC11148773 PMC_DL/PMC11148773/supplementaryfiles/mmc10.xlsx Hsapiens 4 37316 36951 38412 39142"
## [135] "PMC11148773 PMC_DL/PMC11148773/supplementaryfiles/mmc3.xlsx Hsapiens 27 44896 44621 44622 44621 44630 44631 44622 44623 44624 44625 44626 44627 44628 44629 44805 44814 44815 44816 44818 44806 44807 44808 44809 44810 44811 44812 44813"
## [136] "PMC11148058 PMC_DL/PMC11148058/supplementaryfiles/44318_2024_93_MOESM2_ESM.xlsx Hsapiens 26 44451 44446 44448 44266 44453 44442 44449 44263 44259 44264 44444 44443 44258 44257 44531 44445 44441 44450 44256 44260 44265 44262 44256 44261 44440 44257"
## [137] "PMC11148058 PMC_DL/PMC11148058/supplementaryfiles/44318_2024_93_MOESM2_ESM.xlsx Hsapiens 81 44531 44531 44531 44256 44256 44256 44265 44265 44265 44266 44266 44266 44257 44257 44257 44258 44258 44258 44259 44259 44259 44260 44260 44260 44261 44261 44261 44262 44262 44262 44263 44263 44263 44264 44264 44264 44256 44256 44256 44257 44257 44257 44440 44440 44440 44449 44449 44449 44450 44450 44450 44451 44451 44451 44453 44453 44453 44441 44441 44441 44442 44442 44442 44443 44443 44443 44443 44443 44443 44444 44444 44444 44445 44445 44445 44446 44446 44446 44448 44448 44448"
## [138] "PMC11148058 PMC_DL/PMC11148058/supplementaryfiles/44318_2024_93_MOESM2_ESM.xlsx Hsapiens 11 44262 44262 44262 44256 44441 44258 44256 44257 44441 44256 44260"
## [139] "PMC11148058 PMC_DL/PMC11148058/supplementaryfiles/44318_2024_93_MOESM2_ESM.xlsx Hsapiens 81 44531 44531 44531 44256 44256 44256 44265 44265 44265 44266 44266 44266 44257 44257 44257 44258 44258 44258 44259 44259 44259 44260 44260 44260 44261 44261 44261 44262 44262 44262 44263 44263 44263 44264 44264 44264 44256 44256 44256 44257 44257 44257 44440 44440 44440 44449 44449 44449 44450 44450 44450 44451 44451 44451 44453 44453 44453 44441 44441 44441 44442 44442 44442 44443 44443 44443 44443 44443 44443 44444 44444 44444 44445 44445 44445 44446 44446 44446 44448 44448 44448"
## [140] "PMC11148058 zip/Figure_1/1A/YFP-CENPA_Score_from_primary_screen.xlsx Hsapiens 26 44451 44446 44448 44266 44453 44442 44449 44263 44259 44264 44444 44443 44258 44257 44531 44445 44441 44450 44256 44260 44265 44262 44256 44261 44440 44257"
## [141] "PMC11148184 PMC_DL/PMC11148184/supplementaryfiles/44320_2024_32_MOESM2_ESM.xlsx Hsapiens 26 44819 44818 44810 44621 44628 44815 44813 44806 44816 44896 44624 44626 44811 44627 44812 44630 44808 44625 44814 44623 44807 44622 44805 44631 44629 44809"
## [142] "PMC11148184 PMC_DL/PMC11148184/supplementaryfiles/44320_2024_32_MOESM2_ESM.xlsx Hsapiens 26 44450 44453 44445 44263 44256 44454 44448 44451 44441 44531 44264 44261 44259 44447 44260 44446 44262 44258 44449 44257 44265 44444 44443 44442 44440 44266"
## [143] "PMC11148184 PMC_DL/PMC11148184/supplementaryfiles/44320_2024_32_MOESM7_ESM.xlsx Hsapiens 6 44806 44811 44815 44810 44812 44813"
## [144] "PMC11148184 PMC_DL/PMC11148184/supplementaryfiles/44320_2024_32_MOESM7_ESM.xlsx Hsapiens 6 44806 44813 44811 44815 44814 44812"
## [145] "PMC11148184 zip/Figure_5/Figure_5D/2022-9-6-Supplemental-Table-S6.xlsx Hsapiens 6 44806 44811 44815 44810 44812 44813"
## [146] "PMC11148184 zip/Figure_5/Figure_5D/2022-9-6-Supplemental-Table-S6.xlsx Hsapiens 6 44806 44813 44811 44815 44814 44812"
## [147] "PMC11148184 zip/Figure_1/Figure_1F/2022-9-6-Supplemental-Table-S1.xlsx Hsapiens 26 44819 44818 44810 44621 44628 44815 44813 44806 44816 44896 44624 44626 44811 44627 44812 44630 44808 44625 44814 44623 44807 44622 44805 44631 44629 44809"
## [148] "PMC11148184 zip/Figure_1/Figure_1F/2022-9-6-Supplemental-Table-S1.xlsx Hsapiens 26 44450 44453 44445 44263 44256 44454 44448 44451 44441 44531 44264 44261 44259 44447 44260 44446 44262 44258 44449 44257 44265 44444 44443 44442 44440 44266"
## [149] "PMC11148184 zip/Figure_1/Figure_1E/2022-9-6-Supplemental-Table-S1.xlsx Hsapiens 26 44819 44818 44810 44621 44628 44815 44813 44806 44816 44896 44624 44626 44811 44627 44812 44630 44808 44625 44814 44623 44807 44622 44805 44631 44629 44809"
## [150] "PMC11148184 zip/Figure_1/Figure_1E/2022-9-6-Supplemental-Table-S1.xlsx Hsapiens 26 44450 44453 44445 44263 44256 44454 44448 44451 44441 44531 44264 44261 44259 44447 44260 44446 44262 44258 44449 44257 44265 44444 44443 44442 44440 44266"
## [151] "PMC11148184 zip/Figure_3/Figure_3E/2022-9-6-Supplemental-Table-S1.xlsx Hsapiens 26 44819 44818 44810 44621 44628 44815 44813 44806 44816 44896 44624 44626 44811 44627 44812 44630 44808 44625 44814 44623 44807 44622 44805 44631 44629 44809"
## [152] "PMC11148184 zip/Figure_3/Figure_3E/2022-9-6-Supplemental-Table-S1.xlsx Hsapiens 26 44450 44453 44445 44263 44256 44454 44448 44451 44441 44531 44264 44261 44259 44447 44260 44446 44262 44258 44449 44257 44265 44444 44443 44442 44440 44266"
## [153] "PMC11148184 zip/Figure_3/Figure_3F/2022-9-6-Supplemental-Table-S1.xlsx Hsapiens 26 44819 44818 44810 44621 44628 44815 44813 44806 44816 44896 44624 44626 44811 44627 44812 44630 44808 44625 44814 44623 44807 44622 44805 44631 44629 44809"
## [154] "PMC11148184 zip/Figure_3/Figure_3F/2022-9-6-Supplemental-Table-S1.xlsx Hsapiens 26 44450 44453 44445 44263 44256 44454 44448 44451 44441 44531 44264 44261 44259 44447 44260 44446 44262 44258 44449 44257 44265 44444 44443 44442 44440 44266"
## [155] "PMC11148543 PMC_DL/PMC11148543/supplementaryfiles/can-23-2640_supplementary_tables_suppst.xlsx Hsapiens 3 44986 44988 44991"
## [156] "PMC11148543 PMC_DL/PMC11148543/supplementaryfiles/can-23-2640_supplementary_tables_suppst.xlsx Hsapiens 3 44993 44991 44994"
## [157] "PMC11148542 PMC_DL/PMC11148542/supplementaryfiles/mcr-23-0265_supplementary_table_10_suppst10.xlsx Hsapiens 1 40057"
## [158] "PMC11148542 PMC_DL/PMC11148542/supplementaryfiles/mcr-23-0265_supplementary_table_2_suppst2.xlsx Hsapiens 4 36951 40603 37865 40787"
## [159] "PMC11149427 PMC_DL/PMC11149427/supplementaryfiles/Data_Sheet_2.xlsx Hsapiens 4 15-Sep 3-Mar 1-Dec 7-Sep"
## [160] "PMC11149427 PMC_DL/PMC11149427/supplementaryfiles/Data_Sheet_2.xlsx Hsapiens 4 15-Sep 3-Mar 1-Dec 7-Sep"
## [161] "PMC11148150 PMC_DL/PMC11148150/supplementaryfiles/41398_2024_2962_MOESM2_ESM.xlsx Hsapiens 2 44257 44447"
## [162] "PMC11146594 PMC_DL/PMC11146594/supplementaryfiles/Supplemental_Table_2.xlsx Mmusculus 1 39873"
## [163] "PMC11145889 PMC_DL/PMC11145889/supplementaryfiles/12864_2024_10450_MOESM2_ESM.xlsx Hsapiens 116 40057 40057 40057 40057 40057 40057 40057 40787 40057 40057 40057 40057 40057 40057 40057 40057 38231 40057 38961 38777 40057 40787 40057 40057 37226 38596 40787 37681 40057 40057 42248 40787 40422 40057 40057 40057 40057 36951 37681 40057 40057 40787 39508 40603 40057 40057 40057 40057 40057 40238 39692 37681 37316 39873 37681 38047 40787 40787 40057 39508 40057 40057 37865 39692 38047 40057 40057 39873 40057 37500 38777 40238 36951 39692 38777 40238 37681 40057 38231 40057 36951 38047 40787 40057 38047 40057 40238 36951 40603 37316 36951 40057 40057 40057 42248 38231 40238 37226 40057 37316 37226 40057 37135 38961 38231 38961 40057 39508 40057 37865 40238 37316 38047 37316 40057 36951"
## [164] "PMC11145889 PMC_DL/PMC11145889/supplementaryfiles/12864_2024_10450_MOESM2_ESM.xlsx Hsapiens 19 40057 38047 40422 38596 37226 39873 38047 40057 38596 40057 40057 38231 37681 40057 40787 42248 39692 37316 40057"
## [165] "PMC11145889 PMC_DL/PMC11145889/supplementaryfiles/12864_2024_10450_MOESM2_ESM.xlsx Hsapiens 100 40057 37681 40057 40057 37681 39873 38047 36951 40787 36951 40057 38047 37681 36951 40057 36951 39508 38777 40787 40057 37226 38596 40787 37681 40787 36951 37316 38412 37226 36951 37681 37226 39508 39508 36951 37681 37681 40787 37681 40603 39508 40603 40057 38777 36951 37226 37681 39873 37681 38047 38047 40787 37226 38412 37226 40787 36951 39508 38047 36951 39873 38047 38412 38777 38777 37681 39873 38047 36951 37226 38047 40787 37135 36951 38047 38596 40603 37681 40603 38047 40238 37226 37681 38412 39508 38047 38047 37316 37226 37135 37316 40603 38047 38047 40603 37226 40603 39873 36951 36951"
## [166] "PMC11145889 PMC_DL/PMC11145889/supplementaryfiles/12864_2024_10450_MOESM2_ESM.xlsx Ggallus 2 38596 39692"
## [167] "PMC11145787 PMC_DL/PMC11145787/supplementaryfiles/13059_2024_3273_MOESM2_ESM.xlsx Mmusculus 10 94953 94963 94969 94973 94974 94976 94977 94978 94982 94989"
## [168] "PMC11141942 PMC_DL/PMC11141942/supplementaryfiles/jciinsight-9-177697-s073.xlsx Hsapiens 28 44987 45172 45173 44987 45176 45175 44992 45180 44994 45181 44989 44986 44991 45183 45177 44993 45171 45261 44995 44988 45170 45184 44996 45178 45174 44986 45179 44990"
## [169] "PMC11141942 PMC_DL/PMC11141942/supplementaryfiles/jciinsight-9-177697-s073.xlsx Hsapiens 3 45174 45175 45178"
## [170] "PMC11141942 PMC_DL/PMC11141942/supplementaryfiles/jciinsight-9-177697-s073.xlsx Hsapiens 3 45174 45175 45178"
## [171] "PMC10760529 PMC_DL/PMC10760529/supplementaryfiles/Supplemental_Table_S7.xlsx Hsapiens 1 44986"
## [172] "PMC10760529 PMC_DL/PMC10760529/supplementaryfiles/Supplemental_Table_S6.xlsx Hsapiens 2 45232 45233"In depth look at the errors
Let’s investigate the errors in more detail.
# By species
SPECIES <- sapply(strsplit(ERROR_GENELISTS," "),"[[",3)
table(SPECIES)## SPECIES
## Athaliana Dmelanogaster Ggallus Hsapiens Mmusculus
## 9 4 2 106 46
## Rnorvegicus Scerevisiae
## 1 4par(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##
## PMC10756262 PMC10760529 PMC10769850 PMC11141942 PMC11145787 PMC11145889
## 5 2 2 3 1 4
## PMC11146594 PMC11148058 PMC11148150 PMC11148184 PMC11148542 PMC11148543
## 1 5 1 14 2 2
## PMC11148644 PMC11148773 PMC11149427 PMC11150558 PMC11151630 PMC11152081
## 2 3 2 3 1 5
## PMC11153616 PMC11153731 PMC11153834 PMC11157162 PMC11161060 PMC11162794
## 1 1 1 1 2 5
## PMC11162987 PMC11163233 PMC11165217 PMC11165782 PMC11167437 PMC11169032
## 1 1 3 1 1 1
## PMC11170780 PMC11171046 PMC11171932 PMC11172763 PMC11176086 PMC11176395
## 1 1 1 1 1 20
## PMC11178499 PMC11180117 PMC11180607 PMC11181613 PMC11186088 PMC11186173
## 9 2 11 1 2 1
## PMC11186636 PMC11186912 PMC11187367 PMC11187386 PMC11189927 PMC11190204
## 3 1 2 1 4 1
## PMC11190585 PMC11192824 PMC11193738 PMC11194900 PMC11195603 PMC11196711
## 1 1 9 2 7 1
## PMC11197386 PMC11200816 PMC11208570 PMC11209011 PMC11209080 PMC11210073
## 1 1 1 1 5 1
## PMC11212735
## 1summary(as.numeric(DIST))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.00 1.00 1.00 2.82 3.00 20.00hist(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
## 36 PMC11176395 20
## 10 PMC11148184 14
## 39 PMC11180607 11
## 37 PMC11178499 9
## 51 PMC11193738 9
## 53 PMC11195603 7
## 1 PMC10756262 5
## 8 PMC11148058 5
## 18 PMC11152081 5
## 24 PMC11162794 5
## 59 PMC11209080 5
## 6 PMC11145889 4
## 47 PMC11189927 4
## 4 PMC11141942 3
## 14 PMC11148773 3
## 16 PMC11150558 3
## 27 PMC11165217 3
## 43 PMC11186636 3
## 2 PMC10760529 2
## 3 PMC10769850 2MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES## [1] "PMC11176395"# 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## PMC10756262 PMC10760529 PMC10769850 PMC11141942 PMC11145787 PMC11145889
## 57 3 2 34 10 237
## PMC11146594 PMC11148058 PMC11148150 PMC11148184 PMC11148542 PMC11148543
## 1 225 2 284 5 6
## PMC11148644 PMC11148773 PMC11149427 PMC11150558 PMC11151630 PMC11152081
## 4 58 8 75 12 8
## PMC11153616 PMC11153731 PMC11153834 PMC11157162 PMC11161060 PMC11162794
## 2 1 4 1 28 21
## PMC11162987 PMC11163233 PMC11165217 PMC11165782 PMC11167437 PMC11169032
## 3 3 5 2 1 3
## PMC11170780 PMC11171046 PMC11171932 PMC11172763 PMC11176086 PMC11176395
## 2 19 3 1 2 402
## PMC11178499 PMC11180117 PMC11180607 PMC11181613 PMC11186088 PMC11186173
## 60 19 78 3 29 1
## PMC11186636 PMC11186912 PMC11187367 PMC11187386 PMC11189927 PMC11190204
## 42 6 5 1 45 12
## PMC11190585 PMC11192824 PMC11193738 PMC11194900 PMC11195603 PMC11196711
## 7 6 51 51 32 28
## PMC11197386 PMC11200816 PMC11208570 PMC11209011 PMC11209080 PMC11210073
## 1 1 4 16 63 24
## PMC11212735
## 14hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
head(NERR_DF,20)## NERR
## PMC11176395 402
## PMC11148184 284
## PMC11145889 237
## PMC11148058 225
## PMC11180607 78
## PMC11150558 75
## PMC11209080 63
## PMC11178499 60
## PMC11148773 58
## PMC10756262 57
## PMC11193738 51
## PMC11194900 51
## PMC11189927 45
## PMC11186636 42
## PMC11141942 34
## PMC11195603 32
## PMC11186088 29
## PMC11161060 28
## PMC11196711 28
## PMC11210073 24MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR## [1] "PMC11176395"Journals affected
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
### JSON PARSING is more reliable than XML
ARTICLES <- esummary( GENELIST_ERROR_ARTICLES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA$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] 50par(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] "11176395"
##
## $result$`11176395`
## $result$`11176395`$uid
## [1] "11176395"
##
## $result$`11176395`$pubdate
## [1] "2024 Jun 13"
##
## $result$`11176395`$epubdate
## [1] "2024 Jun 13"
##
## $result$`11176395`$printpubdate
## [1] ""
##
## $result$`11176395`$source
## [1] "Nat Commun"
##
## $result$`11176395`$authors
## name authtype
## 1 Al-Kachak A Author
## 2 Di Salvo G Author
## 3 Fulton SL Author
## 4 Chan JC Author
## 5 Farrelly LA Author
## 6 Lepack AE Author
## 7 Bastle RM Author
## 8 Kong L Author
## 9 Cathomas F Author
## 10 Newman EL Author
## 11 Menard C Author
## 12 Ramakrishnan A Author
## 13 Safovich P Author
## 14 Lyu Y Author
## 15 Covington HE 3rd Author
## 16 Shen L Author
## 17 Gleason K Author
## 18 Tamminga CA Author
## 19 Russo SJ Author
## 20 Maze I Author
##
## $result$`11176395`$title
## [1] "Histone serotonylation in dorsal raphe nucleus contributes to stress- and antidepressant-mediated gene expression and behavior."
##
## $result$`11176395`$volume
## [1] "15"
##
## $result$`11176395`$issue
## [1] "1"
##
## $result$`11176395`$pages
## [1] "5042"
##
## $result$`11176395`$articleids
## idtype value
## 1 pmid 38871707
## 2 pmcid PMC11176395
## 3 doi 10.1038/s41467-024-49336-4
## 4 pii 10.1038/s41467-024-49336-4
##
## $result$`11176395`$fulljournalname
## [1] "Nature communications"
##
## $result$`11176395`$sortdate
## [1] "2024/06/13 00:00"
##
## $result$`11176395`$pmclivedate
## [1] "2024/06/14"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] "11176395"
##
## $result$`11176395`
## $result$`11176395`$uid
## [1] "11176395"
##
## $result$`11176395`$pubdate
## [1] "2024 Jun 13"
##
## $result$`11176395`$epubdate
## [1] "2024 Jun 13"
##
## $result$`11176395`$printpubdate
## [1] ""
##
## $result$`11176395`$source
## [1] "Nat Commun"
##
## $result$`11176395`$authors
## name authtype
## 1 Al-Kachak A Author
## 2 Di Salvo G Author
## 3 Fulton SL Author
## 4 Chan JC Author
## 5 Farrelly LA Author
## 6 Lepack AE Author
## 7 Bastle RM Author
## 8 Kong L Author
## 9 Cathomas F Author
## 10 Newman EL Author
## 11 Menard C Author
## 12 Ramakrishnan A Author
## 13 Safovich P Author
## 14 Lyu Y Author
## 15 Covington HE 3rd Author
## 16 Shen L Author
## 17 Gleason K Author
## 18 Tamminga CA Author
## 19 Russo SJ Author
## 20 Maze I Author
##
## $result$`11176395`$title
## [1] "Histone serotonylation in dorsal raphe nucleus contributes to stress- and antidepressant-mediated gene expression and behavior."
##
## $result$`11176395`$volume
## [1] "15"
##
## $result$`11176395`$issue
## [1] "1"
##
## $result$`11176395`$pages
## [1] "5042"
##
## $result$`11176395`$articleids
## idtype value
## 1 pmid 38871707
## 2 pmcid PMC11176395
## 3 doi 10.1038/s41467-024-49336-4
## 4 pii 10.1038/s41467-024-49336-4
##
## $result$`11176395`$fulljournalname
## [1] "Nature communications"
##
## $result$`11176395`$sortdate
## [1] "2024/06/13 00:00"
##
## $result$`11176395`$pmclivedate
## [1] "2024/06/14"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