Gene Name Error Monthly Dashboard
Mark Ziemann
2021-06-10
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("XML")
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.
CURRENT_MONTH=format(Sys.time(), "%m")
CURRENT_YEAR=format(Sys.time(), "%Y")
if (CURRENT_MONTH == "01") {
PREV_YEAR=as.character(as.numeric(format(Sys.time(), "%Y"))-1)
PREV_MONTH="12"
} else {
PREV_YEAR=CURRENT_YEAR
PREV_MONTH=as.character(as.numeric(format(Sys.time(), "%m"))-1)
}
DATE=paste(PREV_YEAR,"/",PREV_MONTH,sep="")
DATE## [1] "2021/5"Let’s see how many PMC IDs we have in the past month.
QUERY ='((genom*[Abstract]))'
ESEARCH_RES <- esearch(term=QUERY, db = "pmc", rettype = "uilist", retmode = "xml", retstart = 0,
retmax = 5000000, usehistory = TRUE, webenv = NULL, querykey = NULL, sort = NULL, field = NULL,
datetype = NULL, reldate = NULL, mindate = DATE, maxdate = DATE)
pmc <- efetch(ESEARCH_RES,retmode="text",rettype="uilist",outfile="pmcids.txt")## Retrieving UIDs 1 to 500## Retrieving UIDs 501 to 1000## Retrieving UIDs 1001 to 1500## Retrieving UIDs 1501 to 2000## Retrieving UIDs 2001 to 2500## Retrieving UIDs 2501 to 3000## Retrieving UIDs 3001 to 3500pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 3160writeLines(pmc,con="pmc.txt")Run the screen
Now run the bash script. Note that false positives can occur (~1.5%) and these results have not been verified by a human.
Here are some definitions:
NUM_XLS = Number of supplementary Excel files in this set of PMC articles.
NUM_XLS_ARTICLES = Number of articles matching the PubMed Central search which have supplementary Excel files.
GENELISTS = The gene lists found in the Excel files. Each Excel file is counted once even it has multiple gene lists.
NUM_GENELISTS = The number of Excel files with gene lists.
NUM_GENELIST_ARTICLES = The number of PMC articles with supplementary Excel gene lists.
ERROR_GENELISTS = Files suspected to contain gene name errors. The dates and five-digit numbers indicate transmogrified gene names.
NUM_ERROR_GENELISTS = Number of Excel gene lists with errors.
NUM_ERROR_GENELIST_ARTICLES = Number of articles with supplementary Excel gene name errors.
ERROR_PROPORTION = This is the proportion of articles with Excel gene lists that have errors.
#system("./gene_names.sh pmc.txt")
results <- readLines("results.txt")
XLS <- results[grep("XLS",results,ignore.case=TRUE)]
NUM_XLS = length(XLS)
NUM_XLS## [1] 4694NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 708GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 588NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 277ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 292GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC8162057" "PMC8157726" "PMC8157653" "PMC8154993" "PMC8154037"
## [6] "PMC8128904" "PMC8152321" "PMC8149607" "PMC8148415" "PMC8144624"
## [11] "PMC8132003" "PMC8116211" "PMC8142489" "PMC8139988" "PMC8131595"
## [16] "PMC8126262" "PMC8121334" "PMC8136213" "PMC8131501" "PMC8134747"
## [21] "PMC8133434" "PMC8131848" "PMC8131847" "PMC8121943" "PMC8121881"
## [26] "PMC8113748" "PMC8104389" "PMC8126652" "PMC8123525" "PMC8120815"
## [31] "PMC8120505" "PMC8119706" "PMC8117642" "PMC8117616" "PMC8124085"
## [36] "PMC8120457" "PMC8120322" "PMC8119999" "PMC8119475" "PMC8119453"
## [41] "PMC8115531" "PMC8113601" "PMC8111777" "PMC8110798" "PMC8102911"
## [46] "PMC8102177" "PMC8090852" "PMC8117591" "PMC8111328" "PMC8115345"
## [51] "PMC8115241" "PMC8104016" "PMC8103922" "PMC8101454" "PMC8092598"
## [56] "PMC8105337" "PMC8104968" "PMC8096971" "PMC8081991" "PMC8076227"
## [61] "PMC8058097" "PMC8055995" "PMC8107818" "PMC8105935" "PMC8097320"
## [66] "PMC8072215" "PMC8063882" "PMC8100660" "PMC8100457" "PMC8100333"
## [71] "PMC8084232" "PMC8084166" "PMC8075899" "PMC8098808" "PMC8098004"
## [76] "PMC8097060" "PMC8096837" "PMC8093579" "PMC8088074" "PMC8065101"
## [81] "PMC8062266" "PMC8062104" "PMC8057611" "PMC8053986" "PMC8052978"
## [86] "PMC8086068" "PMC8046807" "PMC8046804"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 88ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.3176895Look 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] "PMC8162057 /pmc/articles/PMC8162057/bin/Table_1.XLSX Drerio 4 40422 41153 42248 37865"
## [2] "PMC8157726 /pmc/articles/PMC8157726/bin/12862_2021_1830_MOESM9_ESM.xls Scerevisiae 3 43648 43647 43651"
## [3] "PMC8157653 /pmc/articles/PMC8157653/bin/13578_2021_613_MOESM4_ESM.xlsx Hsapiens 23 42627 42430 42429 42622 42435 42614 42623 42429 42434 42431 42620 42619 42618 42436 42433 42437 42613 42616 42438 42621 42430 42617 42615"
## [4] "PMC8157653 /pmc/articles/PMC8157653/bin/13578_2021_613_MOESM5_ESM.xlsx Hsapiens 49 43892 43891 44081 44080 43891 44080 44081 43891 44081 44080 44081 44081 43891 44075 44080 43891 44076 44075 44081 44080 44080 43891 44081 43892 44080 44085 44080 44081 43891 44080 44081 44083 43891 44080 44080 43891 44081 44080 44076 43891 44080 44085 43897 43895 43899 44089 43891 44083 44089"
## [5] "PMC8157653 /pmc/articles/PMC8157653/bin/13578_2021_613_MOESM7_ESM.xlsx Hsapiens 2 44080 44075"
## [6] "PMC8157653 /pmc/articles/PMC8157653/bin/13578_2021_613_MOESM8_ESM.xlsx Hsapiens 3 44077 43900 44085"
## [7] "PMC8154993 /pmc/articles/PMC8154993/bin/41598_2021_90424_MOESM1_ESM.xls Hsapiens 1 2021/03/06"
## [8] "PMC8154037 /pmc/articles/PMC8154037/bin/elife-67624-supp1.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [9] "PMC8128904 /pmc/articles/PMC8128904/bin/42003_2021_2095_MOESM10_ESM.xlsx Hsapiens 2 44079 44077"
## [10] "PMC8152321 /pmc/articles/PMC8152321/bin/12859_2021_4146_MOESM1_ESM.xlsx Hsapiens 1 44257"
## [11] "PMC8149607 /pmc/articles/PMC8149607/bin/Table_2.xlsx Hsapiens 1 43527"
## [12] "PMC8149607 /pmc/articles/PMC8149607/bin/Table_2.xlsx Hsapiens 1 43891"
## [13] "PMC8149607 /pmc/articles/PMC8149607/bin/Table_2.xlsx Hsapiens 1 44078"
## [14] "PMC8149607 /pmc/articles/PMC8149607/bin/Table_2.xlsx Hsapiens 1 44083"
## [15] "PMC8148415 /pmc/articles/PMC8148415/bin/13148_2021_1102_MOESM1_ESM.xlsx Hsapiens 4 44083 44083 43898 44083"
## [16] "PMC8144624 /pmc/articles/PMC8144624/bin/41598_2021_90212_MOESM1_ESM.xlsx Hsapiens 1 40057"
## [17] "PMC8144624 /pmc/articles/PMC8144624/bin/41598_2021_90212_MOESM1_ESM.xlsx Hsapiens 1 40057"
## [18] "PMC8144624 /pmc/articles/PMC8144624/bin/41598_2021_90212_MOESM4_ESM.xlsx Mmusculus 1 37316"
## [19] "PMC8132003 /pmc/articles/PMC8132003/bin/iovs-62-6-18_s010.xlsx Hsapiens 9 38231 39326 38231 39326 40787 39326 37316 37135 38961"
## [20] "PMC8132003 /pmc/articles/PMC8132003/bin/iovs-62-6-18_s011.xlsx Hsapiens 12 37226 40787 39326 40057 37681 38231 37681 38596 40057 40057 40057 40057"
## [21] "PMC8132003 /pmc/articles/PMC8132003/bin/iovs-62-6-18_s012.xlsx Hsapiens 15 38412 39508 38412 39508 40238 38231 37681 39692 39873 41883 39326 38047 39142 40422 37500"
## [22] "PMC8132003 /pmc/articles/PMC8132003/bin/iovs-62-6-18_s012.xlsx Hsapiens 26 37681 39692 37865 38047 39142 40422 37500 38047 39142 40422 37500 38047 39142 37500 40238 38231 36951 37316 40238 38231 40057 37865 38596 40238 38231 40057"
## [23] "PMC8116211 /pmc/articles/PMC8116211/bin/41586_2021_3460_MOESM17_ESM.xlsx Dmelanogaster 4 37500 38596 38231 37135"
## [24] "PMC8142489 /pmc/articles/PMC8142489/bin/12967_2021_2889_MOESM11_ESM.xlsx Hsapiens 41 44085 44075 44077 44085 43892 44085 44084 43892 44078 43891 44085 43891 43892 44085 44085 44084 43899 43901 44075 44085 44075 44076 44075 44085 44079 44083 43892 44084 44089 44085 43892 44077 44089 44076 44084 43897 44081 44085 44075 43899 44079"
## [25] "PMC8142489 /pmc/articles/PMC8142489/bin/12967_2021_2889_MOESM11_ESM.xlsx Hsapiens 41 44085 44075 44077 44085 43892 44085 44084 43892 44078 43891 44085 43891 43892 44085 44085 44084 43899 43901 44075 44085 44075 44076 44075 44085 44079 44083 43892 44084 44089 44085 43892 44077 44089 44076 44084 43897 44081 44085 44075 43899 44079"
## [26] "PMC8142489 /pmc/articles/PMC8142489/bin/12967_2021_2889_MOESM11_ESM.xlsx Hsapiens 8 44086 44086 44083 43893 44083 43898 44083 44075"
## [27] "PMC8142489 /pmc/articles/PMC8142489/bin/12967_2021_2889_MOESM12_ESM.xlsx Hsapiens 132 44078 43900 44080 44080 44080 43893 44080 44080 44080 44080 44080 44080 44080 43898 43898 43898 44077 44077 44077 44080 44080 44080 44080 44080 44082 44082 44077 44077 43894 43893 44077 44077 44080 44080 44080 43898 44076 44076 44083 44083 44083 44083 44083 44088 44081 44081 43900 43892 43892 44080 44080 44080 43896 43896 43896 43893 44084 43894 43892 43898 44082 44082 44082 44082 44083 44083 44083 44083 44083 44083 44083 44083 44083 43894 44082 43900 44080 44080 44080 44080 44080 44080 43898 43893 43893 44077 44077 44083 44083 44083 44083 44083 44083 44083 44083 44083 43894 44088 43898 44085 44085 43900 44082 44082 43899 44080 44082 43894 43891 44084 44084 43898 43893 44083 44083 44083 43900 43900 44079 44077 44088 43898 44082 44082 44082 44082 43892 43892 44077 44077 43895 43895"
## [28] "PMC8142489 /pmc/articles/PMC8142489/bin/12967_2021_2889_MOESM14_ESM.xlsx Hsapiens 2 44081 44075"
## [29] "PMC8142489 /pmc/articles/PMC8142489/bin/12967_2021_2889_MOESM9_ESM.xlsx Hsapiens 1 43892"
## [30] "PMC8139988 /pmc/articles/PMC8139988/bin/41598_2021_89176_MOESM3_ESM.xlsx Hsapiens 10 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951"
## [31] "PMC8139988 /pmc/articles/PMC8139988/bin/41598_2021_89176_MOESM3_ESM.xlsx Hsapiens 10 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951"
## [32] "PMC8139988 /pmc/articles/PMC8139988/bin/41598_2021_89176_MOESM3_ESM.xlsx Hsapiens 2 36951 36951"
## [33] "PMC8139988 /pmc/articles/PMC8139988/bin/41598_2021_89176_MOESM3_ESM.xlsx Hsapiens 2 36951 36951"
## [34] "PMC8139988 /pmc/articles/PMC8139988/bin/41598_2021_89176_MOESM3_ESM.xlsx Hsapiens 2 36951 36951"
## [35] "PMC8139988 /pmc/articles/PMC8139988/bin/41598_2021_89176_MOESM3_ESM.xlsx Hsapiens 2 36951 36951"
## [36] "PMC8139988 /pmc/articles/PMC8139988/bin/41598_2021_89176_MOESM3_ESM.xlsx Hsapiens 28 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865"
## [37] "PMC8131595 /pmc/articles/PMC8131595/bin/41467_2021_23141_MOESM4_ESM.xlsx Hsapiens 1 37681"
## [38] "PMC8126262 /pmc/articles/PMC8126262/bin/peerj-09-11440-s005.xls Mmusculus 1 43896"
## [39] "PMC8126262 /pmc/articles/PMC8126262/bin/peerj-09-11440-s006.xls Rnorvegicus 5 2018/09/09 2018/03/03 2018/03/07 2018/03/08 2018/09/11"
## [40] "PMC8126262 /pmc/articles/PMC8126262/bin/peerj-09-11440-s006.xls Rnorvegicus 3 2018/09/04 2018/03/08 2018/09/06"
## [41] "PMC8121334 /pmc/articles/PMC8121334/bin/pone.0250839.s005.xlsx Hsapiens 25 43533 43718 43527 43716 43715 43525 43722 43526 43710 43713 43532 43529 43719 43530 43531 43528 43526 43525 43535 43709 43720 43723 43717 43534 43714"
## [42] "PMC8136213 /pmc/articles/PMC8136213/bin/12864_2021_7695_MOESM3_ESM.xlsx Celegans 6 43617 43740 43556 43739 43709 43530"
## [43] "PMC8136213 /pmc/articles/PMC8136213/bin/12864_2021_7695_MOESM3_ESM.xlsx Celegans 4 43556 43740 43617 43530"
## [44] "PMC8131501 /pmc/articles/PMC8131501/bin/CTM2-11-e399-s003.xls Hsapiens 6 2021/03/04 2021/03/04 2021/03/04 2021/03/04 2021/09/08 2021/09/04"
## [45] "PMC8134747 /pmc/articles/PMC8134747/bin/Table_6.xlsx Ggallus 26 44077 44083 43899 43901 44084 43900 44080 44082 43897 43891 44075 43892 44078 44085 44166 44088 43893 43898 43896 43894 44079 44076 44081 43895 44086 44089"
## [46] "PMC8134747 /pmc/articles/PMC8134747/bin/Table_6.xlsx Hsapiens 26 44075 43899 43891 43901 43892 44079 44166 43900 44081 44085 44086 43894 43897 44080 43893 44084 44077 44078 44076 44088 44089 44083 43896 44082 43898 43895"
## [47] "PMC8134747 /pmc/articles/PMC8134747/bin/Table_6.xlsx Hsapiens 26 43900 43901 44086 43899 44077 44080 44088 44079 43892 44166 44075 44083 43895 43893 44082 44078 44085 43894 43891 43897 43896 44089 44081 44076 43898 44084"
## [48] "PMC8134747 /pmc/articles/PMC8134747/bin/Table_6.xlsx Hsapiens 26 43900 44082 44079 43899 44075 44086 44083 44088 43894 44080 43893 44077 43897 43896 44081 44078 43901 43891 44076 44085 43892 44166 44084 44089 43898 43895"
## [49] "PMC8134747 /pmc/articles/PMC8134747/bin/Table_6.xlsx Hsapiens 26 43896 44079 43897 44077 43895 43899 44076 43893 43901 44088 44089 44086 44083 44085 44166 43900 43898 44082 43894 44078 43891 44081 44084 44075 44080 43892"
## [50] "PMC8134747 /pmc/articles/PMC8134747/bin/Table_6.xlsx Hsapiens 26 44088 44086 44089 44077 43901 44080 43893 43897 43899 44166 43900 44085 43894 43898 44083 44082 44079 43895 43891 44075 43896 44081 44076 44084 43892 44078"
## [51] "PMC8133434 /pmc/articles/PMC8133434/bin/Table_1.XLSX Hsapiens 1 44264"
## [52] "PMC8133434 /pmc/articles/PMC8133434/bin/Table_2.XLSX Hsapiens 28 44166 43891 43892 43891 43900 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083 43901"
## [53] "PMC8131848 /pmc/articles/PMC8131848/bin/Table_1.xlsx Hsapiens 2 44440 44256"
## [54] "PMC8131847 /pmc/articles/PMC8131847/bin/Table_4.XLS Hsapiens 3 44078 44078 44078"
## [55] "PMC8121943 /pmc/articles/PMC8121943/bin/41467_2021_23124_MOESM4_ESM.xlsx Hsapiens 29 2015-09-01 2002-03-01 2001-03-01 2010-09-01 2007-03-01 2004-03-01 2002-09-01 2011-09-01 2001-03-01 2006-03-01 2011-03-01 2003-03-01 2008-09-01 2007-09-01 2014-09-01 2001-12-01 2008-03-01 2005-03-01 2009-03-01 2012-09-01 2001-09-01 2001-09-01 2004-09-01 2010-03-01 2009-09-01 2002-03-01 2005-09-01 2003-09-01 2006-09-01"
## [56] "PMC8121943 /pmc/articles/PMC8121943/bin/41467_2021_23124_MOESM4_ESM.xlsx Hsapiens 29 2015-09-01 2002-03-01 2001-03-01 2010-09-01 2007-03-01 2004-03-01 2002-09-01 2011-09-01 2001-03-01 2006-03-01 2011-03-01 2003-03-01 2008-09-01 2007-09-01 2014-09-01 2001-12-01 2008-03-01 2005-03-01 2009-03-01 2012-09-01 2001-09-01 2001-09-01 2004-09-01 2010-03-01 2009-09-01 2002-03-01 2005-09-01 2003-09-01 2006-09-01"
## [57] "PMC8121943 /pmc/articles/PMC8121943/bin/41467_2021_23124_MOESM4_ESM.xlsx Hsapiens 28 2015-09-01 2002-03-01 2001-03-01 2010-09-01 2007-03-01 2004-03-01 2002-09-01 2011-09-01 2001-03-01 2006-03-01 2011-03-01 2003-03-01 2008-09-01 2007-09-01 2014-09-01 2001-12-01 2008-03-01 2005-03-01 2009-03-01 2012-09-01 2001-09-01 2001-09-01 2004-09-01 2010-03-01 2009-09-01 2002-03-01 2003-09-01 2006-09-01"
## [58] "PMC8121943 /pmc/articles/PMC8121943/bin/41467_2021_23124_MOESM4_ESM.xlsx Hsapiens 28 2015-09-01 2002-03-01 2001-03-01 2010-09-01 2007-03-01 2004-03-01 2002-09-01 2011-09-01 2001-03-01 2006-03-01 2011-03-01 2003-03-01 2008-09-01 2007-09-01 2014-09-01 2001-12-01 2008-03-01 2005-03-01 2012-09-01 2001-09-01 2001-09-01 2004-09-01 2010-03-01 2009-09-01 2002-03-01 2005-09-01 2003-09-01 2006-09-01"
## [59] "PMC8121943 /pmc/articles/PMC8121943/bin/41467_2021_23124_MOESM4_ESM.xlsx Hsapiens 29 2015-09-01 2002-03-01 2001-03-01 2010-09-01 2007-03-01 2004-03-01 2002-09-01 2011-09-01 2001-03-01 2006-03-01 2011-03-01 2003-03-01 2008-09-01 2007-09-01 2014-09-01 2001-12-01 2008-03-01 2005-03-01 2009-03-01 2012-09-01 2001-09-01 2001-09-01 2004-09-01 2010-03-01 2009-09-01 2002-03-01 2005-09-01 2003-09-01 2006-09-01"
## [60] "PMC8121881 /pmc/articles/PMC8121881/bin/41467_2021_22871_MOESM5_ESM.xlsx Mmusculus 1 43712"
## [61] "PMC8121881 /pmc/articles/PMC8121881/bin/41467_2021_22871_MOESM5_ESM.xlsx Mmusculus 1 43713"
## [62] "PMC8121881 zip/source_data_update/figs3.xlsx Mmusculus 2 44263 44256"
## [63] "PMC8121881 zip/source_data_update/figs3.xlsx Mmusculus 17 44259 44441 44257 44264 44447 44448 44448 44448 44442 44444 44444 44444 44258 44258 44260 44263 44256"
## [64] "PMC8121881 zip/source_data_update/fig4.xlsx Mmusculus 26 44259 44447 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44442 44442 44442 44444 44444 44444"
## [65] "PMC8121881 zip/source_data_update/fig4.xlsx Mmusculus 64 44259 44257 44449 44264 44447 44447 44447 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44266 44266 44266 44261 44261 44261 44261 44261 44257 44260 44260 44260 44262 44262 44262 44262 44262 44450 44453 44263 44263 44263 44263 44440 44256 44256 44256 44256 44256 44256 44256 44446 44446"
## [66] "PMC8121881 zip/source_data_update/fig4.xlsx Mmusculus 2 44263 44256"
## [67] "PMC8121881 zip/source_data_update/fig4.xlsx Mmusculus 2 44443 44444"
## [68] "PMC8113748 /pmc/articles/PMC8113748/bin/mmc3.xlsx Hsapiens 7 39692 41153 40057 39508 37135 39873 37865"
## [69] "PMC8104389 /pmc/articles/PMC8104389/bin/pgen.1009412.s008.xlsx Rnorvegicus 1 44088"
## [70] "PMC8126652 /pmc/articles/PMC8126652/bin/Table_1.xlsx Hsapiens 11 44075 44085 44080 44080 44083 43899 44078 44076 43896 44089 43892"
## [71] "PMC8123525 /pmc/articles/PMC8123525/bin/mmc2.xls Ggallus 8 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/12/01"
## [72] "PMC8123525 /pmc/articles/PMC8123525/bin/mmc2.xls Ggallus 6 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/03/07"
## [73] "PMC8123525 /pmc/articles/PMC8123525/bin/mmc2.xls Ggallus 7 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/03/07 2021/03/07"
## [74] "PMC8120815 /pmc/articles/PMC8120815/bin/12920_2021_975_MOESM2_ESM.xlsx Hsapiens 1 43901"
## [75] "PMC8120815 /pmc/articles/PMC8120815/bin/12920_2021_975_MOESM2_ESM.xlsx Hsapiens 1 44021"
## [76] "PMC8120505 /pmc/articles/PMC8120505/bin/Supplementary_Data2.xlsx Hsapiens 4 44083 43900 44166 44083"
## [77] "PMC8119706 /pmc/articles/PMC8119706/bin/41525_2021_197_MOESM2_ESM.xlsx Hsapiens 8 36951 36951 37226 40603 36951 36951 40603 37226"
## [78] "PMC8119706 /pmc/articles/PMC8119706/bin/41525_2021_197_MOESM3_ESM.xlsx Hsapiens 871 40603 38047 40603 38412 36951 40603 40603 40603 40057 39508 36951 36951 40603 41883 40603 36951 36951 38412 38412 36951 39508 36951 36951 36951 36951 40422 38412 37226 39508 37226 36951 38777 40603 36951 38047 36951 37226 36951 41883 36951 36951 40603 36951 36951 36951 37500 40603 36951 41883 39326 36951 37316 38412 41883 37226 36951 36951 36951 40603 36951 36951 40057 36951 40787 36951 36951 36951 40603 39142 37226 36951 36951 40238 40603 39142 41883 41883 36951 40238 36951 36951 36951 40603 36951 40603 40422 36951 38596 37226 37226 41883 36951 36951 36951 36951 36951 36951 36951 37226 36951 40057 39508 36951 36951 38412 36951 37226 36951 41883 41883 36951 36951 40603 40603 39326 40603 40238 36951 40603 41883 38777 40603 36951 37226 36951 40603 40603 40422 40603 38047 36951 37316 41883 36951 38047 36951 38412 36951 36951 40603 36951 37316 37226 36951 37226 40603 36951 37226 40603 36951 37226 41883 40238 40057 40603 36951 40603 37316 37226 40603 36951 36951 40603 42248 41883 38412 38596 37226 36951 36951 36951 36951 38412 36951 36951 40603 37865 40603 37226 36951 37226 40238 37226 39142 39692 36951 36951 38412 37226 40787 37226 41883 37226 36951 36951 36951 36951 40603 36951 40057 40057 36951 37226 40603 36951 36951 37316 36951 36951 36951 36951 40057 37226 37226 39142 40603 40238 36951 41883 40603 36951 36951 36951 40603 40422 37226 40603 36951 36951 40603 37226 36951 37226 37226 37226 36951 36951 36951 36951 40238 36951 37226 36951 37226 37226 40603 36951 38047 36951 36951 40238 36951 37226 37226 36951 40057 36951 37226 38412 39692 38596 36951 39326 40603 40603 36951 37226 36951 36951 41883 36951 40603 37226 36951 36951 37226 39326 40238 36951 40603 38047 39326 36951 40603 41883 36951 36951 40057 40603 41883 36951 37226 36951 40603 37226 36951 36951 40238 36951 42248 36951 36951 40238 37226 36951 36951 36951 36951 39326 40603 36951 40603 40238 41883 40603 36951 37226 37226 40603 38412 36951 36951 39142 41883 40603 36951 39142 39326 36951 37316 38412 38047 40603 36951 36951 36951 36951 36951 36951 36951 40238 42248 40238 40422 37226 36951 40603 40422 40603 39508 38412 40603 36951 36951 39508 36951 38047 39142 40057 40238 41883 38047 40603 36951 37226 40603 40603 36951 40603 38047 36951 40238 36951 38412 40603 36951 42248 39326 40603 36951 39508 36951 40057 40057 40422 37226 36951 40603 41883 36951 39326 40603 37226 36951 40603 38047 36951 40057 36951 37226 40603 36951 40603 40603 36951 37226 36951 37226 37226 38231 40603 40603 38596 40603 38412 40057 40057 36951 38412 37226 40238 40603 41883 40238 37226 36951 38047 36951 40603 36951 39142 39326 40603 36951 40603 42248 40238 37226 40603 37226 40787 36951 40603 37226 36951 40603 37226 36951 39508 40603 38777 36951 39326 40603 36951 39508 37226 40603 36951 40603 40603 40603 36951 36951 37681 36951 36951 39692 36951 41883 40603 37226 36951 40603 37226 40603 37226 36951 36951 40603 37865 40787 40603 36951 40603 36951 39326 36951 40603 36951 40603 40238 40603 42248 40603 40603 40603 37500 37226 40603 36951 37135 36951 36951 37226 36951 40422 40603 37226 40238 37226 37226 40603 36951 36951 36951 40603 40603 36951 37226 40057 36951 40603 40603 40603 39326 40603 40603 40603 38047 40603 40238 36951 36951 36951 40603 36951 40603 38047 39142 40603 38412 38047 40603 36951 40603 36951 37316 36951 36951 40603 40603 36951 36951 37226 40057 40603 38412 36951 40603 40603 37226 36951 36951 36951 36951 40603 40603 36951 41883 40603 40603 36951 37226 36951 40238 36951 36951 40603 36951 36951 36951 40057 40603 38047 40603 40057 36951 41883 36951 36951 36951 36951 37226 39326 40603 40057 40238 36951 39326 38596 40603 38596 42248 39508 36951 40057 36951 36951 41883 36951 36951 38047 40603 40603 40603 36951 36951 40603 42248 36951 36951 40057 40603 36951 42248 40238 40603 38047 38777 39326 38047 36951 36951 39508 39508 40057 36951 36951 36951 36951 36951 37226 36951 37226 39326 39508 40603 40603 36951 36951 37226 37226 36951 36951 37226 39326 37226 40603 36951 38047 37226 36951 36951 40603 36951 36951 37226 40603 36951 40603 40603 40422 38047 40603 36951 37226 42248 36951 37226 37226 38596 37226 36951 40603 41883 40422 37681 40057 37226 41883 36951 38047 37226 36951 36951 36951 37226 38596 36951 40603 36951 36951 40603 40603 41883 38047 36951 36951 36951 40057 36951 36951 37226 36951 36951 40603 38596 36951 36951 37226 40603 36951 39508 40057 40603 40603 36951 40603 36951 37226 40057 38412 36951 36951 37226 37226 36951 37226 40603 36951 37226 40603 40603 36951 36951 42248 36951 36951 40603 40603 36951 40603 40057 40422 38777 40603 38777 42248 37226 36951 40238 37226 40603 36951 36951 42248 38412 36951 40603 39142 36951 40603 40057 36951 41883 36951 36951 37226 40422 36951 36951 39326 40238 36951 37226 36951 37226 39326 36951 40603 40603 39142 37226 36951 40603 42248 37226 40603 40603 36951 40238 41883 41883 38412 38412 37226 39508 40238 36951 40603 38596 40603 40603 37316 37681 37226 40603 36951 40603 37226 41883 40603 36951 40057 37226 36951 36951 37226 41883 37226 37226 40603 40238 36951 40603 36951 40603 40603 36951 38047 40603 36951 40057 38047 37226 40238 40422 38596 39326 40603 39326 40603 39142 36951 41883 36951 40603 36951 41883 37316 39142 38047 37500 36951 40603 40603 41883 36951 36951 37226"
## [79] "PMC8119706 /pmc/articles/PMC8119706/bin/41525_2021_197_MOESM4_ESM.xlsx Hsapiens 57 38047 36951 36951 40057 40238 37226 40787 40603 39326 36951 39142 37226 38047 40422 37500 39326 38047 40238 39142 36951 42248 37226 36951 37316 40422 40422 36951 37681 36951 38412 40057 36951 37316 38412 40603 36951 40603 36951 40057 37226 36951 37226 36951 39326 38777 37226 39508 41883 37226 40057 40787 37226 40238 41883 36951 36951 40238"
## [80] "PMC8117642 /pmc/articles/PMC8117642/bin/12859_2021_4157_MOESM2_ESM.xlsx Hsapiens 8 44084 44080 44077 43892 44079 44078 44075 43891"
## [81] "PMC8117642 /pmc/articles/PMC8117642/bin/12859_2021_4157_MOESM2_ESM.xlsx Hsapiens 8 44077 44078 43892 44079 44084 44075 44080 43891"
## [82] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM1_ESM.xlsx Hsapiens 23 40057 39326 39142 37316 37500 37135 40422 37681 41883 40787 36951 38231 38777 39692 39508 38961 39873 38412 38596 37316 36951 37865 41153"
## [83] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM1_ESM.xlsx Hsapiens 20 38412 39873 38777 36951 40057 39508 39326 37316 38961 40787 39142 37500 37681 38596 39692 37316 41153 38231 40422 37135"
## [84] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM1_ESM.xlsx Hsapiens 20 39508 38412 37316 39326 40787 40057 37316 39142 36951 39873 38777 37135 41153 37681 38961 37500 38596 38231 40422 39692"
## [85] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM1_ESM.xlsx Hsapiens 25 37316 39508 39326 40787 38412 37316 36951 40057 39692 38961 39873 39142 41153 37681 41883 38777 37500 38231 37135 37865 36951 40422 38047 38596 40238"
## [86] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM3_ESM.xlsx Hsapiens 3 37681 39142 37681"
## [87] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM3_ESM.xlsx Hsapiens 2 38412 38412"
## [88] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM3_ESM.xlsx Hsapiens 2 37316 37316"
## [89] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM3_ESM.xlsx Hsapiens 2 37316 37135"
## [90] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM4_ESM.xlsx Hsapiens 2 39692 37226"
## [91] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM4_ESM.xlsx Hsapiens 21 40057 40057 38961 37865 40787 40057 38961 39326 40057 40057 40057 37500 36951 38596 38596 38412 40057 40057 36951 38412 39508"
## [92] "PMC8117616 /pmc/articles/PMC8117616/bin/12864_2021_7643_MOESM5_ESM.xlsx Hsapiens 18 36951 36951 40238 40057 37865 37135 37500 37316 38777 39142 40238 38596 37681 40238 37316 37681 39692 40603"
## [93] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-2.xls Hsapiens 6 41893 41893 41893 41893 41699 41893"
## [94] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Ggallus 1 45956"
## [95] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 1 43355"
## [96] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Ggallus 1 45956"
## [97] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 3 43346 43164 43160"
## [98] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 1 43355"
## [99] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 2 43355 43161"
## [100] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Ggallus 1 45956"
## [101] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 1 43355"
## [102] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 1 45956"
## [103] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 1 45956"
## [104] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 2 43161 43355"
## [105] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 1 43355"
## [106] "PMC8124085 /pmc/articles/PMC8124085/bin/NIHMS1700548-supplement-4.xlsx Hsapiens 1 43161"
## [107] "PMC8120457 /pmc/articles/PMC8120457/bin/ijbsv17p1744s2.xls Ggallus 1 2020/03/01"
## [108] "PMC8120457 /pmc/articles/PMC8120457/bin/ijbsv17p1744s2.xls Hsapiens 2 2021/03/06 2021/03/06"
## [109] "PMC8120322 /pmc/articles/PMC8120322/bin/Data_Sheet_1.XLSX Hsapiens 27 44257 44256 44442 44441 44445 44261 44531 44265 44263 44447 44451 44448 44440 44258 44450 44256 44446 44266 44264 44257 44444 44262 44443 44260 44453 44449 44259"
## [110] "PMC8120322 /pmc/articles/PMC8120322/bin/Data_Sheet_1.XLSX Hsapiens 27 44450 44261 44441 44448 44259 44449 44447 44446 44263 44260 44262 44445 44258 44444 44264 44257 44257 44442 44440 44256 44453 44443 44256 44265 44451 44266 44531"
## [111] "PMC8119999 /pmc/articles/PMC8119999/bin/Table_3.XLSX Hsapiens 1 03/06/09"
## [112] "PMC8119475 /pmc/articles/PMC8119475/bin/41598_2021_89605_MOESM4_ESM.xlsx Hsapiens 23 44448 44447 44446 44445 44444 44443 44442 44441 44450 44449 44440 44454 44264 44263 44262 44261 44260 44258 44257 44265 44256 44257 44256"
## [113] "PMC8119453 /pmc/articles/PMC8119453/bin/41598_2021_89682_MOESM2_ESM.xlsx Mmusculus 3 43348 43168 43169"
## [114] "PMC8119453 /pmc/articles/PMC8119453/bin/41598_2021_89682_MOESM2_ESM.xlsx Mmusculus 4 43160 43164 43349 43162"
## [115] "PMC8119453 /pmc/articles/PMC8119453/bin/41598_2021_89682_MOESM2_ESM.xlsx Mmusculus 4 43161 43348 43351 43349"
## [116] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM2_ESM.xlsx Hsapiens 30 42622 42622 42622 42439 42620 42622 42434 42435 42436 42624 42622 42619 42621 42430 42622 42624 42432 42622 42437 42624 42624 42622 42432 42430 42705 42620 42439 42440 42620 42620"
## [117] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM2_ESM.xlsx Hsapiens 15 42256 42256 42256 42073 42254 42256 42069 42070 42258 42253 42255 42064 42066 42071 42074"
## [118] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM3_ESM.xlsx Hsapiens 44 42622 42435 42436 42622 42620 42624 42622 42622 42622 42431 42430 42621 42619 42439 42622 42440 42624 42437 42624 42439 42431 42622 42432 42439 42618 42430 42434 42430 42622 42705 42628 42620 42622 42430 42705 42705 42705 42624 42432 42440 42705 42705 42440 42440"
## [119] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM3_ESM.xlsx Hsapiens 20 42622 42435 42436 42622 42620 42624 42622 42622 42431 42430 42621 42619 42622 42437 42439 42431 42432 42618 42705 42440"
## [120] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM5_ESM.xlsx Hsapiens 24 42433 42621 42620 42619 42618 42624 42437 42622 42435 42434 42623 42615 42439 42432 42436 42625 42438 42616 42628 42431 42617 42614 42627 42430"
## [121] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM5_ESM.xlsx Hsapiens 24 42433 42621 42620 42619 42618 42624 42437 42622 42435 42434 42623 42615 42439 42432 42436 42625 42438 42616 42628 42431 42617 42614 42627 42430"
## [122] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM5_ESM.xlsx Hsapiens 24 42433 42621 42620 42619 42618 42624 42437 42622 42435 42434 42623 42615 42439 42432 42436 42625 42438 42616 42628 42431 42617 42614 42627 42430"
## [123] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM5_ESM.xlsx Hsapiens 24 42433 42621 42620 42619 42618 42624 42437 42622 42435 42434 42623 42615 42439 42432 42436 42625 42438 42616 42628 42431 42617 42614 42627 42430"
## [124] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM6_ESM.xlsx Hsapiens 26 42980 42987 42800 42989 42795 42984 42801 42795 42986 42985 42802 42979 42982 42983 42796 42799 42796 42981 42988 42803 42797 42804 42805 42990 42798 43070"
## [125] "PMC8115531 /pmc/articles/PMC8115531/bin/41523_2021_258_MOESM8_ESM.xlsx Hsapiens 25 42987 42982 42802 42981 42990 42805 42980 42979 42801 42803 42797 42989 42983 42986 42800 42984 43070 42985 42799 42795 42988 42796 42798 42804 42992"
## [126] "PMC8113601 /pmc/articles/PMC8113601/bin/41467_2021_22989_MOESM3_ESM.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [127] "PMC8113601 /pmc/articles/PMC8113601/bin/41467_2021_22989_MOESM3_ESM.xlsx Hsapiens 28 44166 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083 43892 43891 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899"
## [128] "PMC8113601 /pmc/articles/PMC8113601/bin/41467_2021_22989_MOESM3_ESM.xlsx Hsapiens 28 43891 44083 44080 44088 43900 43896 44085 43894 43897 44078 44077 43891 44081 43895 44076 44082 44086 44084 43901 43892 43893 43899 44075 44089 43898 44079 43892 44166"
## [129] "PMC8113601 zip/Figure_Raw_Data/1.xlsx Hsapiens 28 44531 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448 44257 44256 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264"
## [130] "PMC8113601 zip/Figure_Raw_Data/S2.xlsx Hsapiens 21 44256 44257 44256 44257 44258 44259 44260 44261 44262 44263 44454 44449 44450 44453 44441 44442 44443 44445 44446 44447 44448"
## [131] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc2.xlsx Mmusculus 16 39326 38231 38231 37500 40057 40057 40057 40057 40057 40057 40422 40422 40422 38596 39326 40057"
## [132] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc2.xlsx Mmusculus 16 39326 38231 38231 37500 40057 40057 40057 40057 40057 40057 40422 40422 40422 38596 39326 40057"
## [133] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc2.xlsx Hsapiens 15 38231 38231 38231 38961 37500 38596 37865 40057 40057 40057 40057 40057 37865 37865 40057"
## [134] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc2.xlsx Hsapiens 15 38231 38231 38231 38961 37500 38596 37865 40057 40057 40057 40057 40057 37865 37865 40057"
## [135] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc2.xlsx Hsapiens 11 38231 37500 39326 37135 39692 38596 40057 40057 38961 39326 37135"
## [136] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc2.xlsx Hsapiens 17 38961 37500 39326 39326 39326 39692 38596 38596 40422 40057 40057 40057 38961 39326 39326 39326 40057"
## [137] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc2.xlsx Hsapiens 17 38961 37500 39326 39326 39326 39692 38596 38596 40422 40057 40057 40057 38961 39326 39326 39326 40057"
## [138] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Mmusculus 13 38231 38231 37500 40057 40057 40057 40057 40057 40422 40422 40422 39326 40057"
## [139] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Mmusculus 15 39326 38231 38231 37500 40057 40057 40057 40057 40057 40057 40422 40422 38596 39326 40057"
## [140] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Ggallus 10 38231 38231 38231 38961 37500 38596 37865 40057 40057 40057"
## [141] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Hsapiens 12 38231 38961 37500 38596 37865 40057 40057 40057 40057 37865 37865 40057"
## [142] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Hsapiens 14 38961 37500 39326 39326 38596 38596 40422 40057 40057 38961 39326 39326 39326 40057"
## [143] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Hsapiens 10 38231 37500 39326 37135 39692 38596 40057 40057 38961 39326"
## [144] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Hsapiens 9 38231 37500 39326 37135 38596 40057 40057 39326 37135"
## [145] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Hsapiens 10 38231 37500 39326 37135 39692 38596 40057 40057 38961 39326"
## [146] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Hsapiens 13 38961 37500 39326 39326 39692 38596 38596 40057 40057 38961 39326 39326 40057"
## [147] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Ggallus 9 38231 37500 39326 37135 38596 40057 40057 39326 37135"
## [148] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Hsapiens 14 38961 37500 39326 39326 38596 38596 40422 40057 40057 38961 39326 39326 39326 40057"
## [149] "PMC8111777 /pmc/articles/PMC8111777/bin/mmc3.xlsx Hsapiens 13 38961 37500 39326 39326 39692 38596 38596 40057 40057 38961 39326 39326 40057"
## [150] "PMC8110798 /pmc/articles/PMC8110798/bin/41467_2021_22338_MOESM3_ESM.xlsx Hsapiens 1 36951"
## [151] "PMC8102911 /pmc/articles/PMC8102911/bin/mmc2.xlsx Hsapiens 1 38231"
## [152] "PMC8102177 /pmc/articles/PMC8102177/bin/mmc2.xlsx Hsapiens 14 37500 39692 40422 37500 40422 40422 40787 37500 40787 40787 37500 40422 40787 39692"
## [153] "PMC8102177 /pmc/articles/PMC8102177/bin/mmc2.xlsx Hsapiens 13 37500 37500 40422 39692 37135 40422 40787 40422 37500 40422 40787 40787 40787"
## [154] "PMC8102177 /pmc/articles/PMC8102177/bin/mmc2.xlsx Hsapiens 11 37500 39692 37500 40422 40422 37135 40787 37500 40787 40422 40787"
## [155] "PMC8090852 /pmc/articles/PMC8090852/bin/EMBJ-40-e106388-s012.xlsx Dmelanogaster 1 38231"
## [156] "PMC8117591 /pmc/articles/PMC8117591/bin/13148_2021_1090_MOESM1_ESM.xlsx Hsapiens 8 43891 43897 44079 43901 43891 44083 43900 44085"
## [157] "PMC8111328 /pmc/articles/PMC8111328/bin/supplementary_table_4.xlsx Hsapiens 5 44075 44080 44079 44085 44084"
## [158] "PMC8115345 /pmc/articles/PMC8115345/bin/41422_2020_401_MOESM11_ESM.xlsx Hsapiens 28 44166 43891 43892 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44089 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [159] "PMC8115241 /pmc/articles/PMC8115241/bin/41422_2020_465_MOESM11_ESM.xlsx Hsapiens 6 44083 43891 43891 43891 43893 43894"
## [160] "PMC8115241 /pmc/articles/PMC8115241/bin/41422_2020_465_MOESM11_ESM.xlsx Hsapiens 7 43893 44085 43892 44081 43893 43893 44166"
## [161] "PMC8104016 /pmc/articles/PMC8104016/bin/hcg-12-e002353-s009.xlsx Hsapiens 4 36951 36951 36951 40238"
## [162] "PMC8104016 /pmc/articles/PMC8104016/bin/hcg-12-e002353-s009.xlsx Hsapiens 3 40238 36951 36951"
## [163] "PMC8104016 /pmc/articles/PMC8104016/bin/hcg-12-e002353-s010.xlsx Hsapiens 14 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951 36951"
## [164] "PMC8103922 /pmc/articles/PMC8103922/bin/peerj-09-11377-s004.xlsx Hsapiens 17 43892 44078 43892 44081 43897 43899 43894 43896 44082 43898 44076 43900 43893 44089 44083 44079 43891"
## [165] "PMC8101454 /pmc/articles/PMC8101454/bin/peerj-09-11342-s013.xlsx Hsapiens 9 44089 43897 43891 43901 44166 43894 43893 43892 43896"
## [166] "PMC8101454 /pmc/articles/PMC8101454/bin/peerj-09-11342-s014.xlsx Hsapiens 31 43896 43897 43895 43893 43900 43898 43899 43900 44166 43894 43897 43897 43897 43891 43896 43895 43897 43898 43901 43899 43891 43896 43891 43891 43896 44089 43896 43896 43892 43893 43898"
## [167] "PMC8092598 /pmc/articles/PMC8092598/bin/pnas.2023157118.sd03.xlsx Hsapiens 3 43891 43895 43896"
## [168] "PMC8105337 /pmc/articles/PMC8105337/bin/41467_2021_22804_MOESM7_ESM.xlsx Hsapiens 14 43710 43719 43531 43717 43717 43714 43709 43714 43714 43709 43715 43717 43714 43525"
## [169] "PMC8105337 /pmc/articles/PMC8105337/bin/41467_2021_22804_MOESM7_ESM.xlsx Hsapiens 28 43714 43717 43714 43717 43715 43723 43529 43715 43714 43717 43723 43529 43530 43531 43525 43525 43715 43717 43714 43723 43709 43525 43715 43717 43714 43723 43715 43714"
## [170] "PMC8104968 /pmc/articles/PMC8104968/bin/elife-65760-supp4.xlsx Hsapiens 16 44080 44082 44076 44084 43895 43896 43892 43893 44083 43892 43897 44078 43891 43891 44081 44085"
## [171] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM10_ESM.xlsx Mmusculus 12 44081 43892 43897 43896 43898 44089 44076 43892 43895 44084 44082 44075"
## [172] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM10_ESM.xlsx Mmusculus 12 44081 44089 43897 43892 44084 44085 43896 43898 44076 43892 44082 43895"
## [173] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM10_ESM.xlsx Mmusculus 13 44089 43892 44076 43895 44085 44082 43892 43898 44084 43897 44075 43896 44081"
## [174] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM10_ESM.xlsx Mmusculus 3 44076 43892 44089"
## [175] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM11_ESM.xlsx Mmusculus 82 44080 44083 44081 44078 44080 44082 43899 44083 44083 43895 43891 43896 44084 43898 43892 43895 44083 43892 43892 43893 44084 44085 44081 44084 43900 44084 43900 43891 44082 44084 43893 43901 43895 44083 43893 44085 43900 44081 43900 43897 44083 44081 43896 43895 44085 43895 43894 43899 43895 43892 43900 43900 43893 43900 43893 44085 43900 43893 43895 43893 44085 43893 43893 43893 43891 43893 44083 43896 43900 43900 43894 43900 43894 43895 44085 43894 43895 43895 43900 44085 43895 43897"
## [176] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM12_ESM.xlsx Mmusculus 83 44083 44083 44079 43895 44083 43895 43900 43892 43892 43892 44083 43896 44083 43896 43895 44084 44081 44085 43893 43895 43895 43900 43895 43900 43893 44084 43900 43891 43897 44080 43897 44083 43897 43891 44083 44078 43894 43898 43899 43895 44085 44078 44082 44083 44083 43899 44081 44084 44077 43901 43892 43900 43891 43898 43898 44084 44084 44082 44084 43900 43892 43892 43895 44083 43893 43895 43896 43892 44081 44083 44084 44084 43893 44085 43893 43895 43895 43898 44085 43895 44084 43900 44085"
## [177] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM4_ESM.xlsx Mmusculus 65 43900 44081 44082 43901 43892 44084 44084 43893 43892 43894 43898 44084 43895 43895 44085 43895 43895 43893 44085 43893 43895 43893 43900 44082 43893 43893 44084 43894 43900 43900 44084 44084 43900 43898 43895 44084 44081 43892 43895 43895 43898 43893 43896 43892 43892 43895 44083 43899 43892 44085 44084 44084 43897 43891 43891 43898 43895 44084 44083 44083 44083 44077 44077 44084 43895"
## [178] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM5_ESM.xlsx Mmusculus 72 43900 44084 43892 44081 43901 44084 44082 44082 43893 43892 43894 43895 43895 44085 44085 43895 43895 43895 43893 43893 43893 43893 43900 44084 44084 43894 43893 43898 43900 43899 43896 44083 44083 43891 44077 43898 44084 44084 44077 43892 43897 43892 44084 44081 44084 43895 43895 43892 43900 44083 43893 44084 44085 43900 43895 44084 43898 43892 43891 44083 43895 43898 43895 43895 44084 44080 43900 44084 44082 43900 44085 43901"
## [179] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM6_ESM.xlsx Mmusculus 1 44082"
## [180] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM6_ESM.xlsx Mmusculus 2 43900 44084"
## [181] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM6_ESM.xlsx Mmusculus 1 44082"
## [182] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM6_ESM.xlsx Mmusculus 3 43894 43893 43898"
## [183] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM6_ESM.xlsx Mmusculus 8 43892 43891 44083 43895 43898 43895 43895 44084"
## [184] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM6_ESM.xlsx Mmusculus 6 43900 43899 43896 44083 44083 43891"
## [185] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM6_ESM.xlsx Mmusculus 1 44080"
## [186] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM7_ESM.xlsx Mmusculus 54 43900 44081 44080 44084 44084 44084 44084 44084 43900 43898 44084 43893 44083 43894 44084 43892 44085 43900 43892 44085 43897 43895 43895 43898 43900 43899 44083 43898 44081 43897 43896 43893 43898 44084 43892 43895 43893 43892 43896 43894 43895 43893 44083 44080 44084 43895 43900 43900 43895 44085 44085 43892 43893 43893"
## [187] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM8_ESM.xlsx Mmusculus 14 43892 44081 43895 43892 43896 44085 43899 43897 44083 43898 44082 44084 44075 44076"
## [188] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM8_ESM.xlsx Mmusculus 14 43895 43896 44085 43892 43898 44084 43897 43899 44075 43892 44081 44076 44083 44082"
## [189] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM8_ESM.xlsx Mmusculus 14 43892 43896 44081 44085 43897 43892 43895 43898 43899 44083 44075 44082 44084 44076"
## [190] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM8_ESM.xlsx Mmusculus 1 43893"
## [191] "PMC8096971 /pmc/articles/PMC8096971/bin/41467_2021_22817_MOESM9_ESM.xlsx Mmusculus 45 44084 44078 43897 43893 44084 43897 43900 43900 43898 44081 44084 44084 43895 43900 44084 43895 44084 43898 43892 43892 43900 44084 44083 43892 43893 44084 44084 44085 43892 43898 43900 44083 43896 44083 43895 44082 44081 44081 44081 43893 43898 44084 43900 44085 43895"
## [192] "PMC8081991 /pmc/articles/PMC8081991/bin/mmc1.xlsx Hsapiens 28 37135 38961 40057 38961 40057 37135 39326 40057 39326 37135 38961 38961 40057 37135 39326 40787 37500 39326 40422 37500 39326 37500 39326 37500 38961 37500 40057 39326"
## [193] "PMC8081991 /pmc/articles/PMC8081991/bin/mmc1.xlsx Hsapiens 57 37135 37500 39326 40787 37316 39692 38412 37316 38412 40787 37316 37316 40057 36951 40787 39326 36951 38777 37500 40787 39326 40422 39508 37681 38777 37500 40787 37135 38412 37135 38412 37135 42248 37500 42248 37500 37135 37135 37135 37135 37135 37500 39142 38777 37135 37500 37135 37135 37135 38412 38777 42248 37135 38412 38777 37135 37135"
## [194] "PMC8081991 /pmc/articles/PMC8081991/bin/mmc1.xlsx Hsapiens 99 37135 42248 37500 42248 37135 37500 37135 37135 37135 37135 38961 37500 40057 42248 38777 39142 36951 37135 42248 40057 38961 37500 36951 38777 37135 37135 39326 37135 38412 42248 37135 42248 38412 38961 39326 37500 40787 40057 37135 38412 42248 38777 39326 40057 38961 39142 37135 40057 42248 38412 38777 38961 39142 42248 39326 37135 39326 37500 40057 42248 37500 40787 37316 39692 38412 40057 42248 38777 37316 38412 39692 40422 40787 37316 40057 39326 42248 38777 37500 40787 36951 42248 40787 37500 39326 39508 38777 40422 37681 40057 40787 42248 38777 39326 37500 37135 42248 38961 37135"
## [195] "PMC8081991 /pmc/articles/PMC8081991/bin/mmc1.xlsx Hsapiens 6 37135 42248 37500 39326 38961 40057"
## [196] "PMC8081991 /pmc/articles/PMC8081991/bin/mmc1.xlsx Hsapiens 12 37500 40787 38777 39326 37500 40057 42248 40057 39326 40787 37500 38777"
## [197] "PMC8076227 /pmc/articles/PMC8076227/bin/41467_2021_22708_MOESM4_ESM.xlsx Hsapiens 6 44449 44446 44441 44448 44450 44447"
## [198] "PMC8076227 /pmc/articles/PMC8076227/bin/41467_2021_22708_MOESM7_ESM.xlsx Hsapiens 15 44256 44257 44256 44265 44257 44258 44259 44263 44449 44450 44442 44443 44444 44445 44447"
## [199] "PMC8076227 /pmc/articles/PMC8076227/bin/41467_2021_22708_MOESM7_ESM.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [200] "PMC8076227 /pmc/articles/PMC8076227/bin/41467_2021_22708_MOESM7_ESM.xlsx Hsapiens 28 44531 44256 44257 44256 44265 44266 44257 44258 44259 44260 44261 44262 44263 44264 44454 44440 44449 44450 44451 44453 44441 44442 44443 44444 44445 44446 44447 44448"
## [201] "PMC8058097 /pmc/articles/PMC8058097/bin/41467_2021_22560_MOESM11_ESM.xlsx Hsapiens 1 41153"
## [202] "PMC8055995 /pmc/articles/PMC8055995/bin/41467_2021_22572_MOESM4_ESM.xlsx Hsapiens 3 43532 43714 43711"
## [203] "PMC8107818 /pmc/articles/PMC8107818/bin/table6.xlsx Hsapiens 12 1-Octen-3-yl-acetate 2,4,6-Octatriene, 2,6-dimethyl-, (E,Z)- 2,4,6-Octatriene, 3,4-dimethyl- 18100 97 2,6-Octadien-1-ol, 3,7-dimethyl-, acetate, (Z)-"
## [204] "PMC8105935 /pmc/articles/PMC8105935/bin/12920_2021_974_MOESM6_ESM.xls Hsapiens 1 44083"
## [205] "PMC8097320 /pmc/articles/PMC8097320/bin/ADVS-8-2004958-s004.xlsx Ggallus 4 43800 43800 43532 43800"
## [206] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd02.xlsx Mmusculus 9 43892 44075 44081 43895 44083 44085 44079 43899 43891"
## [207] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 2 44083 43898"
## [208] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 2 44083 43898"
## [209] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 3 44079 44085 43898"
## [210] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 2 44079 43899"
## [211] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 5 44082 44079 43898 43899 43893"
## [212] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 4 44079 44082 43899 43893"
## [213] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 3 43892 44085 43898"
## [214] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 5 44081 44076 44080 44085 43893"
## [215] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 1 44084"
## [216] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 5 44078 44083 44081 44085 44082"
## [217] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 9 44075 44085 44080 44077 43893 44081 43896 43892 44082"
## [218] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 10 44075 44080 44085 44083 44078 44081 43892 44077 43891 43896"
## [219] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 8 43891 44077 44085 43897 43893 44080 43896 43898"
## [220] "PMC8072215 /pmc/articles/PMC8072215/bin/pnas.2022760118.sd03.xlsx Mmusculus 6 44077 43891 44085 43897 44078 43893"
## [221] "PMC8063882 /pmc/articles/PMC8063882/bin/peerj-09-11272-s006.xlsx Hsapiens 68 43891 43901 44086 43892 44085 43900 43891 43891 44080 43892 43896 43897 44080 44085 43893 43892 43891 44085 43896 43899 44083 44080 43895 43895 44081 43891 44080 43898 44089 44078 43896 44076 44083 43896 43896 44084 44084 44082 44081 43897 44076 43898 43897 44082 44078 44081 44078 44076 44082 44076 44083 43898 44075 44166 44076 44081 43899 44083 43894 43897 43896 44085 43892 43893 44080 43900 44077 43897"
## [222] "PMC8063882 /pmc/articles/PMC8063882/bin/peerj-09-11272-s007.xlsx Hsapiens 27 43893 43891 44083 44075 43900 44081 43897 43892 44077 43901 44080 44084 43894 43899 43895 44166 44078 44088 43891 44082 44085 43896 44076 43901 44089 44086 43898"
## [223] "PMC8063882 /pmc/articles/PMC8063882/bin/peerj-09-11272-s008.xlsx Hsapiens 27 44083 44081 43891 43896 44082 43899 43897 43893 44080 44086 43894 44075 43901 44076 43900 44084 44077 43898 44089 43895 44078 43891 44085 43901 43892 44166 44088"
## [224] "PMC8063882 /pmc/articles/PMC8063882/bin/peerj-09-11272-s009.xlsx Hsapiens 68 43891 43891 44083 44081 43891 43892 43893 43892 43896 44084 43899 44082 43900 44080 43897 44085 44082 43892 43899 44080 44083 44080 44084 44081 44075 44076 44085 44083 43896 43897 44076 44086 43900 44076 43896 44082 44077 43892 43896 44085 43896 44089 43894 44078 44166 44081 43897 43897 43898 43896 44083 43893 44076 43895 44081 43891 44076 44080 44078 44085 44078 43901 44080 43898 43898 43897 43895 43891"
## [225] "PMC8100660 /pmc/articles/PMC8100660/bin/Table_1.xlsx Hsapiens 1 44257"
## [226] "PMC8100660 /pmc/articles/PMC8100660/bin/Table_1.xlsx Hsapiens 1 43892"
## [227] "PMC8100457 /pmc/articles/PMC8100457/bin/table10.xlsx Hsapiens 3 44449 44448 44447"
## [228] "PMC8100457 /pmc/articles/PMC8100457/bin/table11.xlsx Hsapiens 5 44263 44453 44446 44258 44442"
## [229] "PMC8100457 /pmc/articles/PMC8100457/bin/table12.xlsx Hsapiens 3 44265 44257 44259"
## [230] "PMC8100457 /pmc/articles/PMC8100457/bin/table8.xlsx Hsapiens 2 44441 44264"
## [231] "PMC8100457 /pmc/articles/PMC8100457/bin/table9.xlsx Hsapiens 4 44440 44451 44262 44256"
## [232] "PMC8100333 /pmc/articles/PMC8100333/bin/Table_4.xlsx Hsapiens 15 38047 38231 39873 41883 37316 37135 41153 40422 37865 37226 38412 38961 37500 40787 39326"
## [233] "PMC8084232 /pmc/articles/PMC8084232/bin/pone.0250168.s005.xlsx Hsapiens 1 44257"
## [234] "PMC8084232 /pmc/articles/PMC8084232/bin/pone.0250168.s007.xlsx Hsapiens 2 44257 44261"
## [235] "PMC8084166 /pmc/articles/PMC8084166/bin/pgen.1009495.s006.xls Mmusculus 16 44259 44447 44447 44447 44447 44262 44262 44258 44258 44258 44440 44266 44266 44266 44266 44266"
## [236] "PMC8075899 /pmc/articles/PMC8075899/bin/41586_2020_2486_MOESM4_ESM.xlsx Hsapiens 22 37316 36951 40238 40603 37316 37681 38047 38412 38777 39142 39508 37135 40787 41153 41883 37500 37865 38231 38961 39326 39692 40057"
## [237] "PMC8075899 /pmc/articles/PMC8075899/bin/41586_2020_2486_MOESM4_ESM.xlsx Hsapiens 1 37681"
## [238] "PMC8075899 /pmc/articles/PMC8075899/bin/41586_2020_2486_MOESM4_ESM.xlsx Hsapiens 22 37681 38047 36951 38231 37316 39692 38961 37865 39508 39326 40787 38412 41153 40238 39142 40603 37500 37316 38777 37135 40057 41883"
## [239] "PMC8075899 /pmc/articles/PMC8075899/bin/41586_2020_2486_MOESM4_ESM.xlsx Hsapiens 2 39326 40787"
## [240] "PMC8098808 /pmc/articles/PMC8098808/bin/Table_4.XLSX Ggallus 1 44089"
## [241] "PMC8098808 /pmc/articles/PMC8098808/bin/Table_4.XLSX Ggallus 1 43892"
## [242] "PMC8098004 /pmc/articles/PMC8098004/bin/NIHMS1622396-supplement-2.xlsx Hsapiens 2 43717 43718"
## [243] "PMC8097060 /pmc/articles/PMC8097060/bin/41598_2021_89099_MOESM4_ESM.xlsx Hsapiens 27 44166 43900 43901 43891 43892 43893 43894 43895 43896 43897 43898 43899 43891 43892 44084 44085 44075 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [244] "PMC8097060 /pmc/articles/PMC8097060/bin/41598_2021_89099_MOESM5_ESM.xlsx Hsapiens 560 43900 44082 44083 44083 43900 44083 44083 44083 44082 43900 44083 43898 44083 44083 44085 44082 44083 44083 44083 44083 44083 43900 43900 44082 44083 44083 44078 43891 44083 44083 44083 44084 44085 44087 44083 44083 44083 44083 44083 44083 44082 44086 44083 44088 44083 44083 44082 44083 44083 44083 44084 43894 44083 44083 44083 44083 44079 44083 43893 44083 43900 44083 44082 43900 44083 44083 43891 44083 44086 44083 44083 44083 44087 43900 43898 43893 44087 44086 43901 44083 44166 43898 43898 44083 44082 44077 44085 43891 43901 43898 44083 44079 44083 43901 44083 44083 44083 43891 44078 43901 43893 44084 44082 43896 43894 44083 44083 44078 43900 43898 44083 44088 44080 43897 43891 43893 44082 43901 43891 44084 44083 43894 43898 44083 44076 43900 44083 43901 43893 43891 43898 43894 43891 44083 43901 44082 44083 44083 44077 43899 44079 44082 44085 44082 43892 44087 44083 44083 44083 44078 44083 44083 43894 43900 44083 44089 43891 43901 43900 43900 43901 43895 43900 44083 44083 43900 43895 43896 43892 44082 44083 44083 44084 43897 44084 43894 43898 43894 43900 44078 43892 43901 43894 43891 44083 43893 43901 44078 44083 44083 43897 44082 44078 43891 44082 44083 44078 43900 43891 44083 43892 44087 43894 43892 43900 44085 43893 43897 43891 43895 43893 44087 44085 44079 43900 44083 44083 44078 44083 43891 44076 44083 44085 44078 43900 43898 44081 44079 44083 44085 43900 44085 44083 44076 44083 43901 44083 44085 44077 43896 43894 44083 44077 44076 44089 44166 43901 44084 44085 44077 44080 44083 43894 44082 43893 44083 43893 44076 44085 43894 43893 44080 44082 43892 44076 44077 44081 44083 43893 44077 44078 43900 43901 43893 44080 44087 43894 44083 44085 43891 43894 44077 44078 44083 44079 44083 43899 44083 43894 44083 44085 44083 43891 44083 44083 43894 44083 44080 43891 43893 44083 44085 44082 43891 43897 43894 44087 44166 43891 43891 43894 44083 44086 44083 43897 44079 44083 44081 44078 44082 44077 44087 43900 43891 44079 43891 43897 44083 43900 44077 44080 44078 44079 44078 43898 44083 44080 44166 44087 44081 43898 43891 43891 43901 43891 44076 44083 43899 44085 43896 43893 44083 44081 44089 43891 43892 43893 43900 43892 44083 44083 44080 43892 44078 44084 43897 44080 44075 43893 44079 44083 43893 43894 44086 43898 44084 44083 44083 44083 43900 44082 44083 44086 44077 43894 43892 44087 44076 44083 44083 44085 44083 44082 44081 44087 44083 43891 44082 43894 44076 44083 43898 44080 44075 44081 43892 44089 44082 43897 44083 44076 44079 44083 44081 43901 44075 44079 44075 44088 43894 44080 43897 43901 44085 43896 44076 44089 44084 44083 44085 43893 44166 43898 44086 43893 44083 44079 43897 44083 44080 44079 43893 44081 43891 44085 44085 43893 44081 43892 43891 44075 44076 43897 44084 44087 44085 43898 44087 44076 44083 43896 44080 44083 43896 43892 44083 44085 44085 43899 44075 43891 44089 43893 44080 44081 43894 44166 44083 43898 43896 44089 43893 44083 44080 43894 44084 44085 43898 44084 43898 43900 43900 43901 43900 43900 43892 44081 44083 44085 44079 44080 44078 44085 43896 44077 43896 44076 44080 43899 44080 43900 43900 43896 44081 44075 44083 43893 43895 44078 43894 44086 44081 43898 44083 44083 44085 44083 43893 44085 44080 43892 43898 44083 43900 43893 44166 43891 44083 43895 44083 43894 43901 44082 44089 44087 44081 44089 44080 43891 44083 43898 43900 43901 43896 43899 43897 44080 44087 44082 43896"
## [245] "PMC8096837 /pmc/articles/PMC8096837/bin/41598_2021_89131_MOESM1_ESM.xlsx Mmusculus 15 43897 43896 44088 43891 43894 43891 43900 43892 44082 43895 44084 43893 43899 43898 43892"
## [246] "PMC8096837 /pmc/articles/PMC8096837/bin/41598_2021_89131_MOESM1_ESM.xlsx Mmusculus 15 43900 44088 43894 43891 43897 44084 43891 43899 43898 43893 43892 43896 43892 43895 44082"
## [247] "PMC8096837 /pmc/articles/PMC8096837/bin/41598_2021_89131_MOESM1_ESM.xlsx Mmusculus 15 43897 44088 43900 43891 43894 43891 43896 43892 44084 43893 43892 43899 44082 43895 43898"
## [248] "PMC8096837 /pmc/articles/PMC8096837/bin/41598_2021_89131_MOESM1_ESM.xlsx Mmusculus 1 43897"
## [249] "PMC8096837 /pmc/articles/PMC8096837/bin/41598_2021_89131_MOESM2_ESM.xlsx Mmusculus 4 43900 43900 43891 43900"
## [250] "PMC8096837 /pmc/articles/PMC8096837/bin/41598_2021_89131_MOESM2_ESM.xlsx Mmusculus 4 43894 44083 43891 44077"
## [251] "PMC8096837 /pmc/articles/PMC8096837/bin/41598_2021_89131_MOESM2_ESM.xlsx Mmusculus 5 43891 43891 44077 44080 44080"
## [252] "PMC8093579 /pmc/articles/PMC8093579/bin/Data_Sheet_1.xlsx Hsapiens 2 43892 43891"
## [253] "PMC8093579 /pmc/articles/PMC8093579/bin/Data_Sheet_1.xlsx Hsapiens 1 44081"
## [254] "PMC8093579 /pmc/articles/PMC8093579/bin/Data_Sheet_1.xlsx Hsapiens 2 44082 43893"
## [255] "PMC8088074 /pmc/articles/PMC8088074/bin/12859_2021_4142_MOESM3_ESM.xlsx Hsapiens 13 43892 43891 43897 43894 43891 43896 43901 43893 43898 43895 43899 43900 43892"
## [256] "PMC8065101 /pmc/articles/PMC8065101/bin/41523_2021_254_MOESM1_ESM.xlsx Hsapiens 2 37500 40057"
## [257] "PMC8065101 /pmc/articles/PMC8065101/bin/41523_2021_254_MOESM1_ESM.xlsx Hsapiens 9 37500 40057 39326 38777 39142 38412 40787 38961 39692"
## [258] "PMC8065101 /pmc/articles/PMC8065101/bin/41523_2021_254_MOESM1_ESM.xlsx Hsapiens 4 37500 40057 39326 38777"
## [259] "PMC8062266 /pmc/articles/PMC8062266/bin/41388_2021_1738_MOESM4_ESM.xlsx Hsapiens 20 39326 41883 38777 40603 37681 39692 38777 40603 41153 37135 39326 41883 37681 39692 38777 40603 39326 41883 37681 39692"
## [260] "PMC8062104 /pmc/articles/PMC8062104/bin/pgen.1009498.s014.xlsx Mmusculus 3 44079 44075 43898"
## [261] "PMC8062104 /pmc/articles/PMC8062104/bin/pgen.1009498.s014.xlsx Mmusculus 2 44083 43897"
## [262] "PMC8062104 /pmc/articles/PMC8062104/bin/pgen.1009498.s015.xlsx Mmusculus 3 44089 44075 44083"
## [263] "PMC8062104 /pmc/articles/PMC8062104/bin/pgen.1009498.s015.xlsx Mmusculus 3 44078 44083 43892"
## [264] "PMC8062104 /pmc/articles/PMC8062104/bin/pgen.1009498.s016.xlsx Mmusculus 2 38777 39326"
## [265] "PMC8057611 /pmc/articles/PMC8057611/bin/pgen.1009485.s007.xlsx Mmusculus 5 44446 44450 44258 44441 44262"
## [266] "PMC8057611 /pmc/articles/PMC8057611/bin/pgen.1009485.s007.xlsx Mmusculus 7 44451 44444 44265 44257 44257 44448 44443"
## [267] "PMC8057611 /pmc/articles/PMC8057611/bin/pgen.1009485.s008.xlsx Mmusculus 9 44451 44257 44257 44265 44264 44266 44444 44443 44448"
## [268] "PMC8053986 /pmc/articles/PMC8053986/bin/pnas.2001897118.sd01.xlsx Dmelanogaster 4 37500 37135 38231 38596"
## [269] "PMC8053986 /pmc/articles/PMC8053986/bin/pnas.2001897118.sd01.xlsx Dmelanogaster 3 37500 37135 38231"
## [270] "PMC8053986 /pmc/articles/PMC8053986/bin/pnas.2001897118.sd01.xlsx Dmelanogaster 2 37500 37135"
## [271] "PMC8053986 /pmc/articles/PMC8053986/bin/pnas.2001897118.sd01.xlsx Dmelanogaster 1 37500"
## [272] "PMC8053986 /pmc/articles/PMC8053986/bin/pnas.2001897118.sd02.xlsx Dmelanogaster 1 37500"
## [273] "PMC8052978 /pmc/articles/PMC8052978/bin/peerj-09-11259-s002.xlsx Hsapiens 18 43896 44166 43892 43892 43895 43891 44089 43895 43898 43897 43899 43896 43891 43891 43893 43900 43897 43893"
## [274] "PMC8052978 /pmc/articles/PMC8052978/bin/peerj-09-11259-s002.xlsx Hsapiens 1 44166"
## [275] "PMC8086068 /pmc/articles/PMC8086068/bin/13073_2021_880_MOESM2_ESM.xlsx Hsapiens 165 40057 40057 40057 40057 39692 40057 40057 40057 40057 40057 40057 40057 40057 38596 40057 40057 40057 40057 39692 40057 40057 40057 40057 40057 39692 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40787 40787 40787 40787 40787 39692 39692 39692 38961 40057 40057 40057 40057 40057 40057 38961 38961 40057 40057 40057 41153 40057 39692 39692 40057 40057 40057 40057 40057 40057 40057 40057 40057 41153 41153 41153 41153 41153 41153 41153 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 39326 39326 39326 39326 40057 40057 40057 40057 40057 40057 40057 39692 39692 39692 40057 37135 37135 37135 37135 37135 37135 38596 38596 38596 38596 38596 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 39692 39692 39692 40057 40057"
## [276] "PMC8086068 /pmc/articles/PMC8086068/bin/13073_2021_880_MOESM3_ESM.xlsx Hsapiens 46 40057 40057 41153 40057 37135 38596 40787 40057 40057 40057 40057 40057 40057 40057 39692 40057 40057 39326 40057 39692 40057 40057 40057 40057 40057 39692 40057 40057 40057 38961 39692 40057 40057 40057 39692 40057 38961 41153 40057 40057 40057 40057 40057 40057 40057 40057"
## [277] "PMC8046807 /pmc/articles/PMC8046807/bin/42003_2021_1990_MOESM3_ESM.xlsx Rnorvegicus 3 36951 37316 40057"
## [278] "PMC8046807 /pmc/articles/PMC8046807/bin/42003_2021_1990_MOESM3_ESM.xlsx Rnorvegicus 3 36951 37316 40057"
## [279] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Hsapiens 1 37500"
## [280] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Ggallus 1 40057"
## [281] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Hsapiens 1 38596"
## [282] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Hsapiens 1 42248"
## [283] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Hsapiens 1 40787"
## [284] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Hsapiens 1 37500"
## [285] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Hsapiens 1 41883"
## [286] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Hsapiens 1 37500"
## [287] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM11_ESM.xlsx Hsapiens 1 42248"
## [288] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM8_ESM.xlsx Hsapiens 39 41153 43891 43894 44077 43891 43892 43891 44075 43891 38200 44075 44081 44084 43898 44083 43896 44075 44078 43901 44079 1-Dec 44088 43896 44083 44088 44080 44083 43901 44080 43896 43899 44078 44077 38200 44082 44085 44080 43898 43892"
## [289] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM8_ESM.xlsx Hsapiens 6 43525 43525 43530 43722 43534 43714"
## [290] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM8_ESM.xlsx Hsapiens 21 38200 37834 38961 38961 37135 39326 37500 40787 38961 38596 37104 40057 38200 38200 41153 40057 40787 38596 38231 39692 37500"
## [291] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM8_ESM.xlsx Hsapiens 6 37104 40787 37469 38961 37834 38231"
## [292] "PMC8046804 /pmc/articles/PMC8046804/bin/41467_2021_22478_MOESM8_ESM.xlsx Hsapiens 87 37104 37104 37834 37469 37135 41153 37104 41883 41883 37135 37104 42248 40787 38596 38961 38231 37865 37500 37500 37104 40787 37135 38200 41153 37135 37834 38200 37104 37469 37469 37865 37469 37135 39692 42248 38200 37834 41883 41883 38231 38231 40057 37865 38596 37865 37469 38231 37834 38231 38231 37469 38596 39692 37865 38231 39692 37104 37104 37834 40422 39326 38231 38596 37865 37865 38961 37135 38200 37834 37500 39692 38231 38231 41153 37104 37104 38200 38596 37469 40057 37104 40787 41883 38961 39692 38961 40057"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
## Celegans Dmelanogaster Drerio Ggallus Hsapiens
## 2 7 1 14 193
## Mmusculus Rnorvegicus Scerevisiae
## 69 5 1par(mar=c(5,12,4,2))
barplot(table(SPECIES),horiz=TRUE,las=1)
par(mar=c(5,5,4,2))
# Number of affected Excel files per paper
DIST <- table(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
DIST##
## PMC8046804 PMC8046807 PMC8052978 PMC8053986 PMC8055995 PMC8057611 PMC8058097
## 14 2 2 5 1 3 1
## PMC8062104 PMC8062266 PMC8063882 PMC8065101 PMC8072215 PMC8075899 PMC8076227
## 5 1 4 3 15 4 4
## PMC8081991 PMC8084166 PMC8084232 PMC8086068 PMC8088074 PMC8090852 PMC8092598
## 5 1 2 2 1 1 1
## PMC8093579 PMC8096837 PMC8096971 PMC8097060 PMC8097320 PMC8098004 PMC8098808
## 3 7 21 2 1 1 2
## PMC8100333 PMC8100457 PMC8100660 PMC8101454 PMC8102177 PMC8102911 PMC8103922
## 1 5 2 2 3 1 1
## PMC8104016 PMC8104389 PMC8104968 PMC8105337 PMC8105935 PMC8107818 PMC8110798
## 3 1 1 2 1 1 1
## PMC8111328 PMC8111777 PMC8113601 PMC8113748 PMC8115241 PMC8115345 PMC8115531
## 1 19 5 1 2 1 10
## PMC8116211 PMC8117591 PMC8117616 PMC8117642 PMC8119453 PMC8119475 PMC8119706
## 1 1 11 2 3 1 3
## PMC8119999 PMC8120322 PMC8120457 PMC8120505 PMC8120815 PMC8121334 PMC8121881
## 1 2 2 1 2 1 8
## PMC8121943 PMC8123525 PMC8124085 PMC8126262 PMC8126652 PMC8128904 PMC8131501
## 5 3 14 3 1 1 1
## PMC8131595 PMC8131847 PMC8131848 PMC8132003 PMC8133434 PMC8134747 PMC8136213
## 1 1 1 4 2 6 2
## PMC8139988 PMC8142489 PMC8144624 PMC8148415 PMC8149607 PMC8152321 PMC8154037
## 7 6 3 1 4 1 1
## PMC8154993 PMC8157653 PMC8157726 PMC8162057
## 1 4 1 1summary(as.numeric(DIST))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.000 1.000 2.000 3.318 4.000 21.000hist(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
## 24 PMC8096971 21
## 44 PMC8111777 19
## 12 PMC8072215 15
## 1 PMC8046804 14
## 66 PMC8124085 14
## 52 PMC8117616 11
## 49 PMC8115531 10
## 63 PMC8121881 8
## 23 PMC8096837 7
## 78 PMC8139988 7
## 76 PMC8134747 6
## 79 PMC8142489 6
## 4 PMC8053986 5
## 8 PMC8062104 5
## 15 PMC8081991 5
## 30 PMC8100457 5
## 45 PMC8113601 5
## 64 PMC8121943 5
## 10 PMC8063882 4
## 13 PMC8075899 4MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES## [1] "PMC8096971"# 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## PMC8046804 PMC8046807 PMC8052978 PMC8053986 PMC8055995 PMC8057611 PMC8058097
## 168 6 19 11 3 21 1
## PMC8062104 PMC8062266 PMC8063882 PMC8065101 PMC8072215 PMC8075899 PMC8076227
## 13 20 190 15 74 47 77
## PMC8081991 PMC8084166 PMC8084232 PMC8086068 PMC8088074 PMC8090852 PMC8092598
## 202 16 3 211 13 1 3
## PMC8093579 PMC8096837 PMC8096971 PMC8097060 PMC8097320 PMC8098004 PMC8098808
## 5 59 506 587 4 2 2
## PMC8100333 PMC8100457 PMC8100660 PMC8101454 PMC8102177 PMC8102911 PMC8103922
## 15 17 2 40 38 1 17
## PMC8104016 PMC8104389 PMC8104968 PMC8105337 PMC8105935 PMC8107818 PMC8110798
## 21 1 16 42 1 12 1
## PMC8111328 PMC8111777 PMC8113601 PMC8113748 PMC8115241 PMC8115345 PMC8115531
## 5 249 133 7 13 28 256
## PMC8116211 PMC8117591 PMC8117616 PMC8117642 PMC8119453 PMC8119475 PMC8119706
## 4 8 138 16 11 23 936
## PMC8119999 PMC8120322 PMC8120457 PMC8120505 PMC8120815 PMC8121334 PMC8121881
## 1 54 3 4 2 25 115
## PMC8121943 PMC8123525 PMC8124085 PMC8126262 PMC8126652 PMC8128904 PMC8131501
## 143 21 23 9 11 2 6
## PMC8131595 PMC8131847 PMC8131848 PMC8132003 PMC8133434 PMC8134747 PMC8136213
## 1 3 2 62 29 156 10
## PMC8139988 PMC8142489 PMC8144624 PMC8148415 PMC8149607 PMC8152321 PMC8154037
## 56 225 3 4 4 1 28
## PMC8154993 PMC8157653 PMC8157726 PMC8162057
## 1 77 3 4hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
head(NERR_DF,20)## NERR
## PMC8119706 936
## PMC8097060 587
## PMC8096971 506
## PMC8115531 256
## PMC8111777 249
## PMC8142489 225
## PMC8086068 211
## PMC8081991 202
## PMC8063882 190
## PMC8046804 168
## PMC8134747 156
## PMC8121943 143
## PMC8117616 138
## PMC8113601 133
## PMC8121881 115
## PMC8076227 77
## PMC8157653 77
## PMC8072215 74
## PMC8132003 62
## PMC8096837 59MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR## [1] "PMC8119706"Journals affected
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
### JSON PARSING is more reliable than XML
ARTICLES <- esummary( GENELIST_ERROR_ARTICLES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA$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] 43NUM_JOURNALS=length(JOURNALS_TABLE)
par(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] "8096971"
##
## $result$`8096971`
## $result$`8096971`$uid
## [1] "8096971"
##
## $result$`8096971`$pubdate
## [1] "2021 May 4"
##
## $result$`8096971`$epubdate
## [1] "2021 May 4"
##
## $result$`8096971`$printpubdate
## [1] ""
##
## $result$`8096971`$source
## [1] "Nat Commun"
##
## $result$`8096971`$authors
## name authtype
## 1 Little DR Author
## 2 Lynch AM Author
## 3 Yan Y Author
## 4 Akiyama H Author
## 5 Kimura S Author
## 6 Chen J Author
##
## $result$`8096971`$title
## [1] "Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo"
##
## $result$`8096971`$volume
## [1] "12"
##
## $result$`8096971`$issue
## [1] ""
##
## $result$`8096971`$pages
## [1] "2509"
##
## $result$`8096971`$articleids
## idtype value
## 1 pmid 33947861
## 2 doi 10.1038/s41467-021-22817-6
## 3 pmcid PMC8096971
##
## $result$`8096971`$fulljournalname
## [1] "Nature Communications"
##
## $result$`8096971`$sortdate
## [1] "2021/05/04 00:00"
##
## $result$`8096971`$pmclivedate
## [1] "2021/05/11"Paper with most date conversions
MOST_ERR <- gsub("PMC","",MOST_ERR)
ARTICLE_DATA <- esummary(MOST_ERR,db = "pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLE_DATA,as= "parsed")
ARTICLE_DATA## $header
## $header$type
## [1] "esummary"
##
## $header$version
## [1] "0.3"
##
##
## $result
## $result$uids
## [1] "8119706"
##
## $result$`8119706`
## $result$`8119706`$uid
## [1] "8119706"
##
## $result$`8119706`$pubdate
## [1] "2021 May 13"
##
## $result$`8119706`$epubdate
## [1] "2021 May 13"
##
## $result$`8119706`$printpubdate
## [1] ""
##
## $result$`8119706`$source
## [1] "NPJ Genom Med"
##
## $result$`8119706`$authors
## name authtype
## 1 Juul RI Author
## 2 Nielsen MM Author
## 3 Juul M Author
## 4 Feuerbach L Author
## 5 Pedersen JS Author
##
## $result$`8119706`$title
## [1] "The landscape and driver potential of site-specific hotspots across cancer genomes"
##
## $result$`8119706`$volume
## [1] "6"
##
## $result$`8119706`$issue
## [1] ""
##
## $result$`8119706`$pages
## [1] "33"
##
## $result$`8119706`$articleids
## idtype value
## 1 pmid 33986299
## 2 doi 10.1038/s41525-021-00197-6
## 3 pmcid PMC8119706
##
## $result$`8119706`$fulljournalname
## [1] "NPJ Genomic Medicine"
##
## $result$`8119706`$sortdate
## [1] "2021/05/13 00:00"
##
## $result$`8119706`$pmclivedate
## [1] "2021/05/17"Trend info
To plot the trend over the past 6-12 months.
url <- "http://ziemann-lab.net/public/gene_name_errors/"
doc <- htmlParse(url)
links <- xpathSApply(doc, "//a/@href")
links <- links[grep("html",links)]
links## href href href
## "Report_2021-02.html" "Report_2021-03.html" "Report_2021-04.html"
## href
## "Report_2021-05.html"unlink("online_files/",recursive=TRUE)
dir.create("online_files")
sapply(links, function(mylink) {
download.file(paste(url,mylink,sep=""),destfile=paste("online_files/",mylink,sep=""))
} )## href href href href
## 0 0 0 0myfilelist <- list.files("online_files/",full.names=TRUE)
trends <- sapply(myfilelist, function(myfilename) {
x <- readLines(myfilename)
# Num XL gene list articles
NUM_GENELIST_ARTICLES <- x[grep("NUM_GENELIST_ARTICLES",x)[3]+1]
NUM_GENELIST_ARTICLES <- sapply(strsplit(NUM_GENELIST_ARTICLES," "),"[[",3)
NUM_GENELIST_ARTICLES <- sapply(strsplit(NUM_GENELIST_ARTICLES,"<"),"[[",1)
NUM_GENELIST_ARTICLES <- as.numeric(NUM_GENELIST_ARTICLES)
# number of affected articles
NUM_ERROR_GENELIST_ARTICLES <- x[grep("NUM_ERROR_GENELIST_ARTICLES",x)[3]+1]
NUM_ERROR_GENELIST_ARTICLES <- sapply(strsplit(NUM_ERROR_GENELIST_ARTICLES," "),"[[",3)
NUM_ERROR_GENELIST_ARTICLES <- sapply(strsplit(NUM_ERROR_GENELIST_ARTICLES,"<"),"[[",1)
NUM_ERROR_GENELIST_ARTICLES <- as.numeric(NUM_ERROR_GENELIST_ARTICLES)
# Error proportion
ERROR_PROPORTION <- x[grep("ERROR_PROPORTION",x)[3]+1]
ERROR_PROPORTION <- sapply(strsplit(ERROR_PROPORTION," "),"[[",3)
ERROR_PROPORTION <- sapply(strsplit(ERROR_PROPORTION,"<"),"[[",1)
ERROR_PROPORTION <- as.numeric(ERROR_PROPORTION)
# number of journals
NUM_JOURNALS <- x[grep('JOURNALS_TABLE',x)[3]+1]
NUM_JOURNALS <- sapply(strsplit(NUM_JOURNALS," "),"[[",3)
NUM_JOURNALS <- sapply(strsplit(NUM_JOURNALS,"<"),"[[",1)
NUM_JOURNALS <- as.numeric(NUM_JOURNALS)
NUM_JOURNALS
res <- c(NUM_GENELIST_ARTICLES,NUM_ERROR_GENELIST_ARTICLES,ERROR_PROPORTION,NUM_JOURNALS)
return(res)
})
colnames(trends) <- sapply(strsplit(colnames(trends),"_"),"[[",3)
colnames(trends) <- gsub(".html","",colnames(trends))
trends <- as.data.frame(trends)
rownames(trends) <- c("NUM_GENELIST_ARTICLES","NUM_ERROR_GENELIST_ARTICLES","ERROR_PROPORTION","NUM_JOURNALS")
trends <- t(trends)
trends <- as.data.frame(trends)
CURRENT_RES <- c(NUM_GENELIST_ARTICLES,NUM_ERROR_GENELIST_ARTICLES,ERROR_PROPORTION,NUM_JOURNALS)
trends <- rbind(trends,CURRENT_RES)
paste(CURRENT_YEAR,CURRENT_MONTH,sep="-")## [1] "2021-06"rownames(trends)[nrow(trends)] <- paste(CURRENT_YEAR,CURRENT_MONTH,sep="-")
plot(trends$NUM_GENELIST_ARTICLES, xaxt = "n" , type="b" , main="Number of articles with Excel gene lists per month",
ylab="number of articles", xlab="month")
axis(1, at=1:nrow(trends), labels=rownames(trends))
plot(trends$NUM_ERROR_GENELIST_ARTICLES, xaxt = "n" , type="b" , main="Number of articles with gene name errors per month",
ylab="number of articles", xlab="month")
axis(1, at=1:nrow(trends), labels=rownames(trends))
plot(trends$ERROR_PROPORTION, xaxt = "n" , type="b" , main="Proportion of articles with Excel gene list affected by errors",
ylab="proportion", xlab="month")
axis(1, at=1:nrow(trends), labels=rownames(trends))
plot(trends$NUM_JOURNALS, xaxt = "n" , type="b" , main="Number of journals with affected articles",
ylab="number of journals", xlab="month")
axis(1, at=1:nrow(trends), labels=rownames(trends))
unlink("online_files/")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 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] readxl_1.3.1 reutils_0.2.3 xml2_1.3.2 jsonlite_1.7.2 XML_3.99-0.6
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.6 knitr_1.33 magrittr_2.0.1 R6_2.5.0
## [5] rlang_0.4.11 stringr_1.4.0 highr_0.9 tools_4.1.0
## [9] xfun_0.23 jquerylib_0.1.4 htmltools_0.5.1.1 yaml_2.2.1
## [13] digest_0.6.27 assertthat_0.2.1 sass_0.4.0 bitops_1.0-7
## [17] RCurl_1.98-1.3 evaluate_0.14 rmarkdown_2.8 stringi_1.6.2
## [21] compiler_4.1.0 bslib_0.2.5.1 cellranger_1.1.0