Gene Name Error Monthly Dashboard
Mark Ziemann
2021-06-08
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="2021/2"Let’s see how many PMC IDs we have in the past month.
QUERY ='((genom*[Abstract]))'
ESEARCH_RES <- esearch(term=QUERY, db = "pmc", rettype = "uilist", retmode = "xml", retstart = 0,
retmax = 5000000, usehistory = TRUE, webenv = NULL, querykey = NULL, sort = NULL, field = NULL,
datetype = NULL, reldate = NULL, mindate = 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 3000pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 2632writeLines(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] 3318NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 575GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 470NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 214ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 219GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC7908713" "PMC7903802" "PMC7893923" "PMC7890893" "PMC7887196"
## [6] "PMC7884730" "PMC7884410" "PMC7881617" "PMC7881115" "PMC7881037"
## [11] "PMC7880998" "PMC7878750" "PMC7896317" "PMC7885916" "PMC7876146"
## [16] "PMC7876141" "PMC7874467" "PMC7871411" "PMC7896349" "PMC7870932"
## [21] "PMC7870011" "PMC7894049" "PMC7893110" "PMC7865055" "PMC7865025"
## [26] "PMC7864951" "PMC7863008" "PMC7888619" "PMC7863452" "PMC7862275"
## [31] "PMC7861379" "PMC7861375" "PMC7866887" "PMC7859232" "PMC7887632"
## [36] "PMC7884756" "PMC7884045" "PMC7880683" "PMC7854732" "PMC7882740"
## [41] "PMC7851759" "PMC7116828" "PMC7851345" "PMC7851772" "PMC7875399"
## [46] "PMC7846840" "PMC7845134" "PMC7876278" "PMC7844411" "PMC7844020"
## [51] "PMC7873973" "PMC7846933" "PMC7868554" "PMC7862794" "PMC7862768"
## [56] "PMC7859520" "PMC7859435" "PMC7880367" "PMC7880322" "PMC7845975"
## [61] "PMC7845644" "PMC7848703" "PMC7848201" "PMC7808690" "PMC7877913"
## [66] "PMC7874222" "PMC7873862" "PMC7868925" "PMC7834956" "PMC7880379"
## [71] "PMC7876704" "PMC7834090" "PMC7889151" "PMC7671374" "PMC7854777"
## [76] "PMC7850965"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 76ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.3551402Look 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] "PMC7908713 /pmc/articles/PMC7908713/bin/13073_2021_852_MOESM2_ESM.xlsx Hsapiens 20 40238 39142 36951 37500 37865 38047 41883 39508 37316 38231 40787 38777 40603 38596 40422 37316 39692 37135 40057 38412"
## [2] "PMC7908713 /pmc/articles/PMC7908713/bin/13073_2021_852_MOESM3_ESM.xlsx Hsapiens 28 37865 40238 40603 36951 39142 40057 41883 39508 40422 38596 39692 37316 36951 38231 40787 41153 37316 39326 37500 37681 37135 38961 39873 38412 38047 38777 42248 37226"
## [3] "PMC7908713 /pmc/articles/PMC7908713/bin/13073_2021_852_MOESM3_ESM.xlsx Hsapiens 28 37316 39142 37865 40238 40603 41883 38777 36951 38596 40422 39508 38047 40057 36951 38231 41153 39692 39326 40787 37681 38961 37500 37135 37316 38412 39873 42248 37226"
## [4] "PMC7908713 zip/Supplementary_table_S1.xlsx Hsapiens 26 40057 37226 37316 40422 37681 39142 37500 37865 41883 36951 40238 40603 38047 38412 38777 39508 39873 42248 37135 40787 41153 38231 38596 38961 39326 39692"
## [5] "PMC7908713 zip/Supplementary_table_S1.xlsx Hsapiens 26 38047 37316 37865 40238 39142 37226 36951 40603 37681 38412 38777 39508 39873 42248 37135 40422 40787 41153 41883 37500 38231 38596 38961 39326 39692 40057"
## [6] "PMC7903802 /pmc/articles/PMC7903802/bin/12864_2021_7438_MOESM2_ESM.xlsx Scerevisiae 1 37165"
## [7] "PMC7893923 /pmc/articles/PMC7893923/bin/13058_2021_1402_MOESM1_ESM.xlsx Hsapiens 20 43526 43526 43526 43527 43527 43529 43529 43530 43531 43723 43719 43710 43710 43711 43711 43713 43714 43715 43716 43717"
## [8] "PMC7893923 /pmc/articles/PMC7893923/bin/13058_2021_1402_MOESM1_ESM.xlsx Hsapiens 19 43526 43526 43527 43527 43529 43529 43530 43531 43533 43723 43719 43710 43710 43710 43711 43711 43713 43715 43717"
## [9] "PMC7893923 /pmc/articles/PMC7893923/bin/13058_2021_1402_MOESM1_ESM.xlsx Hsapiens 19 43526 43526 43527 43527 43529 43529 43530 43531 43532 43533 43723 43719 43710 43710 43711 43713 43714 43715 43717"
## [10] "PMC7890893 /pmc/articles/PMC7890893/bin/13046_2021_1865_MOESM5_ESM.xlsx Hsapiens 2 43891 43892"
## [11] "PMC7887196 /pmc/articles/PMC7887196/bin/41598_2021_82877_MOESM2_ESM.xlsx Ggallus 27 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 41153 37135 37135 38231 40238 40057 37316 38596 37865"
## [12] "PMC7887196 /pmc/articles/PMC7887196/bin/41598_2021_82877_MOESM2_ESM.xlsx Ggallus 28 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 41153 37135 37135 38231 40238 40057 37316 38596 37865 37865"
## [13] "PMC7887196 /pmc/articles/PMC7887196/bin/41598_2021_82877_MOESM2_ESM.xlsx Ggallus 28 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 41153 37135 37135 38231 40238 40057 37316 38596 37865 37865"
## [14] "PMC7884730 /pmc/articles/PMC7884730/bin/41525_2021_177_MOESM6_ESM.xlsx Hsapiens 27 2-Mar 3-Sep 4-Sep 2-Mar 7-Sep 6-Sep 7-Mar 11-Sep 9-Mar 12-Sep 4-Mar 1-Mar 6-Mar 14-Sep 8-Sep 8-Mar 2-Sep 1-Dec 10-Mar 3-Mar 1-Sep 11-Mar 9-Sep 5-Sep 1-Mar 10-Sep 5-Mar"
## [15] "PMC7884410 /pmc/articles/PMC7884410/bin/41398_2021_1248_MOESM3_ESM.xlsx Hsapiens 27 44076 44077 44082 44086 44084 44081 43891 44089 43893 44083 43901 43897 43894 43892 44088 43891 43900 44078 44085 43896 44166 44075 43892 44075 43898 43895 43899"
## [16] "PMC7881617 /pmc/articles/PMC7881617/bin/12967_2021_2733_MOESM1_ESM.xlsx Hsapiens 3 44089 43891 43892"
## [17] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM11_ESM.xlsx Mmusculus 13 40057 37135 38412 37500 38596 37316 39326 39873 39142 38777 40787 37316 38961"
## [18] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM11_ESM.xlsx Mmusculus 15 40787 38961 40057 39142 38596 39873 37316 38412 37500 37681 38231 37135 38777 37316 39326"
## [19] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM11_ESM.xlsx Mmusculus 16 40422 37135 39326 40787 38596 39692 40057 37316 39873 37500 38961 37316 38777 39142 38412 38231"
## [20] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 97 40238 38961 37681 37681 40057 39142 37865 38777 37681 36951 38961 40057 38961 40057 38961 40787 37681 37681 38047 39326 38961 38961 40787 40057 39326 36951 37135 39692 38231 37681 40057 36951 40422 40057 40057 40057 40057 36951 40787 40057 37500 36951 37681 40057 40057 40057 40057 40057 40787 40787 37135 40057 38596 37316 37316 40057 40787 37681 40787 40057 40787 37135 40057 37316 37135 38596 40787 37316 38961 40057 40057 37316 40057 39873 40057 36951 40057 40057 37500 40057 40057 36951 40057 40787 40057 39873 40057 40057 37681 37681 39326 40057 40057 39873 38777 39873 40057"
## [21] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 29 38961 38961 40238 40238 39142 38777 38596 38047 38596 38231 38777 39326 41883 37316 38596 38777 37316 38777 36951 37316 37500 37681 37681 39692 38596 37316 41883 38047 39873"
## [22] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 42 40238 39142 37681 36951 37681 36951 41153 37681 37681 37865 39873 37135 37681 39142 38777 37316 37316 37681 40057 39873 40422 37681 39142 39142 37681 36951 37681 40603 41883 39142 37681 37681 38047 37500 40603 38777 37681 39326 36951 37316 38047 37681"
## [23] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 121 40238 38961 37316 40238 40238 38961 38961 38777 37681 37681 40057 37681 37681 39142 38961 37681 39326 40238 40238 38777 39326 38047 39692 38047 40057 38961 37681 37681 38961 38231 40057 37681 40787 40057 40057 37681 40057 38961 38231 40057 39326 40787 40787 39326 40787 40787 40057 39873 36951 40057 40057 38961 40057 37135 40057 40057 38777 40057 40057 37500 40057 40057 40787 40057 40057 40057 40057 39873 38777 40057 36951 40057 37316 37316 40057 40057 40057 39873 40057 40057 40057 37865 37681 37316 40057 40057 38596 39873 37500 40787 37135 36951 40057 39873 39326 40057 38596 38777 40057 40787 37135 37316 40787 40057 40057 40057 38961 40057 39142 37316 40057 40787 40787 40057 40057 36951 37135 39692 40787 40422 37681"
## [24] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 36 36951 38777 38961 38596 38047 40057 40238 40238 40238 38777 38231 39326 37316 39692 40238 40057 38777 37681 38777 38777 38777 41883 36951 38596 37316 36951 40057 38596 38596 37500 40057 39873 40057 41883 38596 38047"
## [25] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 58 39692 37316 39142 39326 37681 37681 40238 36951 40603 40057 37681 40057 38047 40603 37681 37681 37681 40238 40603 40603 37865 39873 38777 39142 37865 37681 40422 37135 37681 37681 37135 37681 41153 39142 36951 36951 37316 37681 37500 38047 37681 37316 39326 36951 40603 37681 37681 37316 41883 37681 39142 38047 40057 40603 37681 37681 37500 38777"
## [26] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 100 38231 39142 36951 40238 40057 37681 37681 40057 40238 37316 37681 39692 40057 40057 37316 38047 40057 40057 37681 38047 40057 39692 40057 40057 37681 38231 40057 40057 40057 36951 40057 40057 37135 40057 40057 40057 37681 40057 40057 40057 38777 36951 36951 40238 40057 40787 38961 37316 40057 40057 40057 39692 40057 40057 38961 40057 39873 38961 37316 40787 40787 38777 40238 40787 37316 37135 37316 40057 40057 38596 40057 40787 38596 40057 40057 38777 40057 37135 40057 37500 39326 38961 40057 40057 37681 37681 38777 40787 40057 37135 40057 40787 37681 40787 37500 39873 40057 39873 38961 40787"
## [27] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 28 40057 36951 38777 38596 38777 39692 38777 38961 37316 37316 38777 37681 36951 38777 37500 40238 39873 41883 38596 38047 39326 38231 38596 39142 40238 40057 40238 41883"
## [28] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 52 39326 40057 39326 36951 40603 40422 36951 38047 37316 40603 37681 38047 37681 40057 37681 38047 40238 37316 39142 40057 37681 37681 37681 36951 37135 37681 37681 37681 40238 41883 40238 38777 37316 39142 37681 37500 41153 37865 39142 36951 37681 37500 39142 37135 37865 39692 37681 39142 37681 40603 37681 39873"
## [29] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 114 37865 40238 36951 40057 36951 39142 37681 37681 40057 37681 40057 36951 37316 36951 40057 38961 40057 40057 39326 40057 40057 37135 40057 40057 40057 38231 40057 40787 38047 40057 40057 40057 37681 40057 40057 40057 39692 37681 40422 37316 40787 36951 39692 40057 40057 40787 40057 40057 37865 40057 38961 38961 40057 38961 37135 38777 40787 37316 40057 40057 37135 40057 40057 37681 37681 38961 38777 39326 39326 39873 37316 40057 40057 38961 39873 40787 39142 40787 37681 40057 40787 39326 37681 40787 39873 38777 40787 38961 38596 40787 40422 37681 40057 40057 38961 38961 37500 40787 40057 36951 37135 40057 38777 37316 37681 40787 38961 37681 37500 40057 38596 37681 39326 39873"
## [30] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 38 40238 40238 40057 40238 36951 38777 40057 38596 38596 40238 38596 36951 38777 38596 38596 41883 38047 40057 37316 39873 38961 39326 38047 38961 38777 40057 38777 37500 37316 38777 37681 38231 38596 37316 41883 39692 37681 37316"
## [31] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM3_ESM.xlsx Mmusculus 55 39326 40238 40057 40057 37316 40422 39142 38047 36951 39142 37316 38047 41153 36951 37316 37681 41883 37681 37681 37681 37681 36951 37681 37681 36951 39142 37681 41153 37681 40603 38777 38047 39142 39142 37865 38047 40603 39142 37681 37681 37681 37681 39873 38777 37135 37681 37681 40603 37316 37865 37681 40603 39873 37500 40603"
## [32] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM6_ESM.xlsx Mmusculus 15 40787 38961 39326 37135 38777 37681 39142 40057 38596 37316 37316 37500 38412 39873 38231"
## [33] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM7_ESM.xlsx Mmusculus 1 39142"
## [34] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM8_ESM.xlsx Mmusculus 117 40057 37681 37865 40787 40787 38961 40787 37681 38777 40057 37316 39326 38961 37681 39692 36951 39692 40057 39142 37681 40787 38961 40422 40787 40057 37681 40057 40787 38961 40057 36951 39326 40057 40057 39142 37135 37135 37681 40057 40057 40057 38596 40057 40057 38961 40057 39873 37316 40057 39873 39326 37316 40057 37500 37681 40057 38961 40057 40057 37681 37681 37135 38961 38777 40787 38777 40057 40057 40057 38047 37316 37681 38961 40057 40057 37316 39142 40057 40057 40787 37681 40057 38596 39142 40057 38961 39326 40787 40057 36951 39873 40238 37865 38777 36951 40787 37135 40787 40057 40057 40057 39873 38961 40787 39326 37500 39873 38231 40057 40787 40057 37681 38961 40057 37316 40787 38961"
## [35] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM8_ESM.xlsx Mmusculus 37 40238 40057 38596 40238 40057 41883 38596 40057 38231 38596 38777 38777 38047 39692 38596 38596 38777 40057 41883 37316 40057 36951 38961 39326 38777 38777 38777 37500 37681 36951 38231 39873 37316 38047 37316 40238 40238"
## [36] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM8_ESM.xlsx Mmusculus 56 39142 39142 40057 37681 38777 38047 40238 37865 39326 37135 36951 39142 39142 40422 37681 41883 37681 39142 36951 37316 39142 37681 37681 37681 40057 37681 39873 37681 38047 41153 37681 37681 38047 40603 40603 40603 37681 40057 37681 37865 38777 40603 37316 37316 37316 40603 37681 37135 37681 41153 37681 37681 37500 36951 37681 37681"
## [37] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM8_ESM.xlsx Mmusculus 104 36951 40057 37681 37681 40057 40057 40057 37316 36951 36951 39692 40787 37681 38961 38777 40057 40057 40057 37135 38961 38231 36951 40057 38777 40787 39326 40057 40787 40057 40057 40422 37135 40057 40057 38777 40057 40057 40057 40057 40057 37681 40057 40057 37316 40787 38961 40057 37316 37135 40057 40057 40057 40057 40057 36951 39873 40057 37865 40057 40057 40057 40787 38777 36951 40057 40787 37316 40787 40057 36951 38961 39873 39142 40057 36951 39142 39326 40787 40057 38961 37135 36951 40787 37681 38596 40787 37681 38047 37681 39873 40057 40057 37681 37500 39326 37316 39326 38961 38961 39873 38777 38961 37500 40057"
## [38] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM8_ESM.xlsx Mmusculus 32 38961 38596 40057 38596 38777 41883 40238 38596 40057 38596 40057 37316 37316 39326 38961 38596 38777 37316 38047 41883 37316 37681 38231 38777 39873 40238 37500 38777 38047 37681 36951 39692"
## [39] "PMC7881115 /pmc/articles/PMC7881115/bin/41467_2021_21109_MOESM8_ESM.xlsx Mmusculus 47 40057 36951 37316 37865 41153 40238 37681 40422 37500 36951 39142 39142 38777 39873 39326 37681 36951 37681 39142 38047 37316 39142 41153 37681 37681 38047 37681 37681 37316 36951 37681 39142 40603 38777 37681 40603 39873 37681 41883 37681 37681 37135 40603 37681 37681 37500 39142"
## [40] "PMC7881037 /pmc/articles/PMC7881037/bin/42003_2021_1722_MOESM4_ESM.xlsx Hsapiens 81 44089 44089 43892 43892 43891 44084 44084 43897 43897 43897 43894 43894 44076 44076 44085 44085 44085 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43896 43896 43896 43901 43901 43893 43893 43893 44082 44081 44081 44081 44088 44088 44166 44166 44166 44166 44166 44166 44166 43898 43898 43898 43898 43895 43895 43899 43899 43899 44086 44075 43900 43900 43900 43900 44083 44083 44083 44083 44083 44083 43892 44079 44077 44080 44080 44080"
## [41] "PMC7881037 /pmc/articles/PMC7881037/bin/42003_2021_1722_MOESM4_ESM.xlsx Hsapiens 81 44089 44089 43892 43892 43891 44084 44084 43897 43897 43897 43894 43894 44076 44076 44085 44085 44085 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43896 43896 43896 43901 43901 43893 43893 43893 44082 44081 44081 44081 44088 44088 44166 44166 44166 44166 44166 44166 44166 43898 43898 43898 43898 43895 43895 43899 43899 43899 44086 44075 43900 43900 43900 43900 44083 44083 44083 44083 44083 44083 43892 44079 44077 44080 44080 44080"
## [42] "PMC7881037 /pmc/articles/PMC7881037/bin/42003_2021_1722_MOESM4_ESM.xlsx Hsapiens 81 44089 44089 43892 43892 43891 44084 44084 43897 43897 43897 43894 43894 44076 44076 44085 44085 44085 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43896 43896 43896 43901 43901 43893 43893 43893 44082 44081 44081 44081 44088 44088 44166 44166 44166 44166 44166 44166 44166 43898 43898 43898 43898 43895 43895 43899 43899 43899 44086 44075 43900 43900 43900 43900 44083 44083 44083 44083 44083 44083 43892 44079 44077 44080 44080 44080"
## [43] "PMC7881037 /pmc/articles/PMC7881037/bin/42003_2021_1722_MOESM4_ESM.xlsx Hsapiens 81 44089 44089 43892 43892 43891 44084 44084 43897 43897 43897 43894 43894 44076 44076 44085 44085 44085 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43896 43896 43896 43901 43901 43893 43893 43893 44082 44081 44081 44081 44088 44088 44166 44166 44166 44166 44166 44166 44166 43898 43898 43898 43898 43895 43895 43899 43899 43899 44086 44075 43900 43900 43900 43900 44083 44083 44083 44083 44083 44083 43892 44079 44077 44080 44080 44080"
## [44] "PMC7881037 /pmc/articles/PMC7881037/bin/42003_2021_1722_MOESM4_ESM.xlsx Hsapiens 81 44089 44089 43892 43892 43891 44084 44084 43897 43897 43897 43894 43894 44076 44076 44085 44085 44085 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43891 43896 43896 43896 43901 43901 43893 43893 43893 44082 44081 44081 44081 44088 44088 44166 44166 44166 44166 44166 44166 44166 43898 43898 43898 43898 43895 43895 43899 43899 43899 44086 44075 43900 43900 43900 43900 44083 44083 44083 44083 44083 44083 43892 44079 44077 44080 44080 44080"
## [45] "PMC7880998 /pmc/articles/PMC7880998/bin/41467_2021_21255_MOESM13_ESM.xlsx Hsapiens 27 44082 44080 43892 44081 44076 43893 43898 44078 43900 44083 43891 43892 44077 44075 44086 44085 43891 43895 43897 44084 43894 44166 44088 43899 43896 43901 44089"
## [46] "PMC7880998 /pmc/articles/PMC7880998/bin/41467_2021_21255_MOESM13_ESM.xlsx Hsapiens 27 44082 44080 43892 44081 44076 43893 43898 44078 43900 44083 43891 43892 44077 44075 44086 44085 43891 43895 43897 44084 43894 44166 44088 43899 43896 43901 44089"
## [47] "PMC7878750 /pmc/articles/PMC7878750/bin/41467_2021_21213_MOESM4_ESM.xlsx Hsapiens 28 43892 44075 44086 44089 43893 43892 44081 43895 43891 43898 43897 44076 43901 44080 44088 43899 44082 44085 44084 43900 43891 43894 43896 44077 44166 44079 44083 44078"
## [48] "PMC7896317 /pmc/articles/PMC7896317/bin/pnas.2016648118.sd01.xlsx Hsapiens 3 43895 43891 44085"
## [49] "PMC7896317 /pmc/articles/PMC7896317/bin/pnas.2016648118.sd01.xlsx Mmusculus 16 43529 43525 43719 43526 43715 43710 43531 43723 43714 43526 43532 43530 43716 43717 43533 43711"
## [50] "PMC7896317 /pmc/articles/PMC7896317/bin/pnas.2016648118.sd01.xlsx Mmusculus 1 44085"
## [51] "PMC7885916 /pmc/articles/PMC7885916/bin/media-5.xlsx Hsapiens 192 44257 44256 44262 44256 44441 44256 44441 44256 44441 44440 44262 44257 44448 44441 44264 44448 44257 44256 44446 44256 44263 44256 44261 44257 44257 44257 44257 44258 44263 44450 44264 44450 44448 44256 44264 44264 44441 44261 44450 44257 44450 44446 44262 44257 44258 44258 44446 44264 44264 44258 44448 44257 44258 44256 44256 44257 44257 44257 44256 44264 44264 44441 44450 44446 44264 44263 44257 44261 44441 44441 44263 44262 44260 44448 44257 44258 44256 44261 44450 44441 44264 44446 44262 44440 44256 44448 44256 44256 44445 44264 44264 44258 44256 44448 44448 44450 44263 44258 44264 44450 44441 44260 44441 44448 44260 44264 44264 44258 44258 44440 44262 44257 44440 44445 44260 44448 44256 44256 44262 44448 44256 44258 44257 44256 44445 44258 44261 44262 44441 44261 44256 44257 44261 44263 44258 44258 44441 44260 44256 44263 44441 44256 44257 44258 44256 44440 44263 44257 44256 44258 44260 44256 44263 44256 44445 44262 44258 44448 44446 44256 44256 44263 44262 44446 44441 44264 44263 44258 44450 44258 44262 44258 44448 44256 44261 44256 44263 44446 44257 44256 44257 44441 44264 44258 44262 44264 44258 44262 44262 44446 44262 44256"
## [52] "PMC7885916 /pmc/articles/PMC7885916/bin/media-5.xlsx Hsapiens 104 44264 44263 44440 44261 44263 44262 44257 44257 44261 44262 44257 44257 44263 44262 44260 44450 44257 44260 44450 44264 44264 44445 44264 44261 44441 44260 44450 44264 44261 44257 44262 44261 44264 44260 44263 44261 44257 44264 44262 44261 44261 44448 44450 44263 44260 44260 44264 44264 44261 44262 44264 44262 44260 44260 44261 44260 44261 44262 44261 44263 44261 44441 44264 44441 44448 44448 44263 44261 44261 44261 44450 44262 44260 44264 44263 44264 44257 44260 44260 44257 44445 44257 44264 44445 44260 44264 44262 44260 44450 44441 44262 44446 44262 44264 44264 44262 44261 44448 44261 44257 44263 44257 44261 44263"
## [53] "PMC7885916 /pmc/articles/PMC7885916/bin/media-5.xlsx Hsapiens 109 44264 44257 44260 44263 44263 44261 44261 44257 44446 44450 44445 44261 44448 44261 44264 44257 44262 44262 44260 44261 44450 44263 44264 44257 44262 44450 44264 44262 44262 44441 44441 44446 44448 44257 44262 44448 44263 44262 44446 44262 44260 44263 44261 44264 44261 44264 44260 44445 44260 44263 44262 44262 44264 44257 44262 44448 44448 44264 44264 44261 44450 44262 44257 44257 44257 44448 44262 44262 44450 44450 44263 44260 44262 44257 44264 44257 44261 44264 44263 44262 44264 44257 44264 44262 44264 44448 44262 44263 44257 44260 44264 44262 44264 44263 44441 44263 44264 44263 44448 44257 44263 44257 44264 44261 44264 44448 44262 44262 44260"
## [54] "PMC7885916 /pmc/articles/PMC7885916/bin/media-5.xlsx Hsapiens 76 44260 44440 44256 44260 44257 44450 44440 44445 44440 44261 44445 44441 44450 44441 44440 44257 44262 44450 44440 44440 44260 44256 44450 44440 44440 44261 44260 44450 44448 44262 44450 44440 44262 44261 44256 44450 44440 44262 44440 44261 44262 44256 44450 44440 44256 44257 44261 44450 44257 44448 44261 44448 44260 44450 44256 44262 44256 44440 44260 44262 44262 44256 44261 44256 44256 44450 44450 44262 44440 44256 44440 44440 44450 44261 44262 44450"
## [55] "PMC7885916 /pmc/articles/PMC7885916/bin/media-5.xlsx Hsapiens 150 44261 44450 44441 44264 44441 44264 44260 44450 44261 44448 44258 44258 44263 44258 44450 44441 44450 44263 44448 44441 44257 44448 44263 44258 44450 44264 44441 44262 44445 44263 44440 44264 44261 44445 44258 44448 44261 44264 44264 44262 44262 44441 44448 44440 44262 44264 44450 44257 44262 44264 44450 44448 44264 44258 44262 44257 44261 44264 44263 44262 44441 44263 44264 44262 44450 44441 44448 44262 44450 44257 44262 44262 44441 44448 44262 44262 44450 44450 44441 44263 44262 44262 44262 44258 44441 44261 44446 44262 44440 44450 44441 44448 44263 44262 44261 44263 44257 44450 44257 44258 44264 44264 44263 44440 44450 44440 44263 44261 44264 44262 44261 44258 44264 44263 44448 44448 44264 44441 44264 44264 44441 44445 44258 44263 44262 44448 44448 44450 44258 44263 44450 44264 44264 44262 44264 44441 44263 44441 44448 44260 44264 44260 44257 44262 44262 44258 44258 44450 44258 44261"
## [56] "PMC7885916 /pmc/articles/PMC7885916/bin/media-5.xlsx Hsapiens 170 44261 44257 44257 44449 44262 44449 44261 44449 44449 44260 44262 44257 44449 44257 44257 44264 44261 44257 44261 44257 44260 44260 44260 44449 44257 44446 44258 44261 44263 44448 44262 44445 44445 44262 44261 44261 44261 44257 44257 44262 44258 44262 44449 44440 44264 44262 44261 44257 44448 44449 44264 44258 44449 44441 44260 44441 44264 44262 44261 44261 44441 44264 44449 44449 44258 44440 44262 44264 44264 44449 44445 44257 44449 44446 44446 44261 44261 44450 44261 44262 44258 44261 44257 44449 44263 44263 44260 44257 44260 44258 44263 44261 44257 44261 44263 44257 44257 44449 44258 44260 44440 44260 44257 44262 44258 44263 44448 44257 44257 44262 44258 44262 44261 44261 44257 44257 44258 44449 44263 44257 44257 44440 44257 44264 44258 44440 44262 44260 44264 44264 44264 44441 44263 44258 44264 44260 44446 44261 44260 44448 44260 44261 44261 44263 44262 44257 44257 44441 44262 44440 44448 44262 44262 44263 44263 44261 44261 44257 44261 44449 44262 44449 44257 44262 44264 44440 44262 44263 44257 44264"
## [57] "PMC7876146 /pmc/articles/PMC7876146/bin/41467_2020_20585_MOESM11_ESM.xlsx Hsapiens 26 43527 43531 43529 43720 43712 43525 43718 43709 43722 43711 43534 43716 43710 43535 43532 43528 43525 43800 43526 43526 43533 43717 43723 43719 43715 43530"
## [58] "PMC7876141 /pmc/articles/PMC7876141/bin/41467_2021_21081_MOESM10_ESM.xlsx Hsapiens 5 43717 43531 43527 43526 43532"
## [59] "PMC7876141 /pmc/articles/PMC7876141/bin/41467_2021_21081_MOESM10_ESM.xlsx Hsapiens 42 42987 42987 42987 42987 42987 42987 42987 42987 42987 42987 42987 42987 42987 42987 42987 42987 42987 42801 42801 42987 42987 42801 42801 42801 42987 42987 42801 42987 42987 42987 42801 42801 42987 42987 42987 42801 42987 42987 42987 42987 42987 42987"
## [60] "PMC7876141 /pmc/articles/PMC7876141/bin/41467_2021_21081_MOESM10_ESM.xlsx Hsapiens 30 42802 42796 42802 42796 42796 42802 42796 42802 42796 42802 42796 42802 42796 42802 42796 42802 42796 42796 42796 42802 42796 42802 42796 42802 42796 42796 42802 42796 42796 42802"
## [61] "PMC7876141 /pmc/articles/PMC7876141/bin/41467_2021_21081_MOESM5_ESM.xlsx Hsapiens 5 43533 43533 43533 43533 43533"
## [62] "PMC7874467 /pmc/articles/PMC7874467/bin/13100_2021_233_MOESM6_ESM.xlsx Hsapiens 16 44076 43892 44084 44077 44085 44081 44080 43897 43896 44082 43892 43891 43895 44083 43899 43898"
## [63] "PMC7874467 /pmc/articles/PMC7874467/bin/13100_2021_233_MOESM6_ESM.xlsx Hsapiens 16 44076 44081 43892 44085 43896 44080 44084 43897 44077 43892 43891 43899 43898 44082 43895 44083"
## [64] "PMC7874467 /pmc/articles/PMC7874467/bin/13100_2021_233_MOESM6_ESM.xlsx Hsapiens 17 43896 44081 44076 44085 43892 44077 44080 44084 43898 43897 43892 44075 44082 43899 44083 43895 43891"
## [65] "PMC7874467 /pmc/articles/PMC7874467/bin/13100_2021_233_MOESM6_ESM.xlsx Hsapiens 19 44085 44076 44081 43892 44083 43899 44080 44084 43897 43896 43898 44075 43891 43892 43893 44077 44082 43891 43895"
## [66] "PMC7871411 /pmc/articles/PMC7871411/bin/12864_2021_7416_MOESM18_ESM.xlsx Athaliana 1 43711"
## [67] "PMC7896349 /pmc/articles/PMC7896349/bin/pnas.2019789118.sd02.xlsx Hsapiens 6 3-deoxy-2-octulosonic acid(2)-lipid A 3-deoxy-2-octulosonic acid(2)-lipid A"
## [68] "PMC7870932 /pmc/articles/PMC7870932/bin/41467_2021_21177_MOESM3_ESM.xlsx Hsapiens 2 43898 43893"
## [69] "PMC7870932 /pmc/articles/PMC7870932/bin/41467_2021_21177_MOESM3_ESM.xlsx Hsapiens 3 44075 43898 43893"
## [70] "PMC7870011 /pmc/articles/PMC7870011/bin/pone.0246443.s021.xlsx Hsapiens 18 43719 43719 43532 43531 43529 43534 43722 43528 43711 43722 43713 43713 43713 43710 43710 43526 43526 43526"
## [71] "PMC7870011 /pmc/articles/PMC7870011/bin/pone.0246443.s026.xlsx Hsapiens 23 42797 42992 42992 42796 42796 42796 42980 42980 42983 42983 42983 42989 42989 42800 42801 42801 42798 42798 42804 42984 42984 42984 43714"
## [72] "PMC7894049 /pmc/articles/PMC7894049/bin/Table_1.XLSX Hsapiens 13 43891 43891 44084 44080 44081 43892 43896 44083 44077 43899 44082 44076 43898"
## [73] "PMC7894049 /pmc/articles/PMC7894049/bin/Table_2.XLSX Hsapiens 14 44080 44084 43891 43892 44082 43891 44081 44083 44077 44089 44075 43892 43896 44085"
## [74] "PMC7893110 /pmc/articles/PMC7893110/bin/Table_6.XLSX Hsapiens 7 43898 43892 43893 43897 43896 43899 43895"
## [75] "PMC7865055 /pmc/articles/PMC7865055/bin/41467_2021_21064_MOESM6_ESM.xlsx Hsapiens 1 44079"
## [76] "PMC7865025 /pmc/articles/PMC7865025/bin/41467_2020_20870_MOESM5_ESM.xlsx Hsapiens 1 43891"
## [77] "PMC7865025 /pmc/articles/PMC7865025/bin/41467_2020_20870_MOESM7_ESM.xlsx Ggallus 1 44083"
## [78] "PMC7865025 /pmc/articles/PMC7865025/bin/41467_2020_20870_MOESM9_ESM.xlsx Hsapiens 1 43896"
## [79] "PMC7864951 /pmc/articles/PMC7864951/bin/41598_2020_80857_MOESM1_ESM.xlsx Hsapiens 2 43530 43717"
## [80] "PMC7863008 /pmc/articles/PMC7863008/bin/MSB-17-e9866-s004.xlsx Dmelanogaster 6 44166 44075 44076 44079 44078 44078"
## [81] "PMC7863008 /pmc/articles/PMC7863008/bin/MSB-17-e9866-s005.xlsx Dmelanogaster 5 44076 44079 44166 44078 44075"
## [82] "PMC7863008 /pmc/articles/PMC7863008/bin/MSB-17-e9866-s006.xlsx Dmelanogaster 4 44075 44076 44078 44079"
## [83] "PMC7863008 /pmc/articles/PMC7863008/bin/MSB-17-e9866-s007.xlsx Dmelanogaster 2 44078 44078"
## [84] "PMC7888619 /pmc/articles/PMC7888619/bin/pgen.1009309.s032.xlsx Hsapiens 1 43710"
## [85] "PMC7863452 /pmc/articles/PMC7863452/bin/12920_2021_883_MOESM5_ESM.xls Hsapiens 7 40057 40057 40057 40057 40057 40057 40057"
## [86] "PMC7862275 /pmc/articles/PMC7862275/bin/41698_2021_144_MOESM5_ESM.xlsx Hsapiens 5 37834 37469 38200 37104 36892"
## [87] "PMC7861379 /pmc/articles/PMC7861379/bin/pone.0246603.s009.xls Hsapiens 48 38419 38606 38657 38598 38606 38416 38602 38419 38603 38597 38597 38415 38417 38418 38610 38418 38601 38416 38413 38601 38597 38601 38417 38606 38597 38603 38417 38606 38606 38601 38420 38420 38601 38444 38603 38601 38601 38687 38599 38599 38414 38601 38604 38605 38604 38596 38604 38605"
## [88] "PMC7861379 /pmc/articles/PMC7861379/bin/pone.0246603.s010.xls Hsapiens 33 40787 40787 41153 40057 40057 39692 39692 37865 40787 37500 40057 38961 38961 39326 38961 42248 37500 37500 38231 39326 37135 38961 37500 39692 40422 38231 37500 39326 40422 38231 38961 40057 40787"
## [89] "PMC7861379 /pmc/articles/PMC7861379/bin/pone.0246603.s011.xls Hsapiens 33 38231 39326 38961 37135 41153 38231 39326 37500 40787 37865 39692 42248 40057 40422 39692 40057 38231 40787 38961 40422 39692 38961 40057 37500 37500 39326 38961 38961 40787 37500 40057 37500 40787"
## [90] "PMC7861375 /pmc/articles/PMC7861375/bin/ppat.1009244.s001.xlsx Hsapiens 144 44166 44166 44166 43892 43892 43892 43900 43900 43900 43901 43901 43901 43893 43893 43893 43894 43894 43894 43895 43895 43895 43896 43896 43896 43897 43897 43897 43898 43898 43898 43899 43899 43899 44088 44088 44088 44089 44089 44089 44084 44084 44084 44085 44085 44085 44086 44086 44086 44076 44076 44076 44077 44077 44077 44078 44078 44078 44079 44079 44079 44080 44080 44080 44081 44081 44081 44082 44082 44082 44083 44083 44083 44166 44166 44166 43892 43892 43892 43900 43900 43900 43901 43901 43901 43893 43893 43893 43894 43894 43894 43895 43895 43895 43896 43896 43896 43897 43897 43897 43898 43898 43898 43899 43899 43899 44089 44089 44089 44084 44084 44084 44085 44085 44085 44086 44086 44086 44088 44088 44088 44076 44076 44076 44077 44077 44077 44078 44078 44078 44079 44079 44079 44080 44080 44080 44081 44081 44081 44082 44082 44082 44083 44083 44083"
## [91] "PMC7861375 /pmc/articles/PMC7861375/bin/ppat.1009244.s002.xls Hsapiens 21 44166 43893 44085 43897 43900 44081 43894 43892 44082 44083 44088 44086 44080 43899 43898 44089 43896 44076 44079 44084 44078"
## [92] "PMC7861375 /pmc/articles/PMC7861375/bin/ppat.1009244.s003.xls Hsapiens 17 43896 43898 43901 43895 44083 43900 44077 44082 43894 44088 43897 43899 44166 44079 43892 44080 44085"
## [93] "PMC7866887 /pmc/articles/PMC7866887/bin/peerj-09-10560-s006.xlsx Hsapiens 52 43710 43526 43525 43712 43525 43718 43531 43717 43525 43710 43712 43710 43533 43532 43718 43720 43526 43534 43529 43527 43723 43532 43718 43529 43528 43532 43722 43526 43527 43714 43527 43530 43800 43711 43711 43530 43709 43526 43714 43713 43722 43719 43714 43530 43719 43709 43715 43712 43535 43713 43710 43526"
## [94] "PMC7866887 /pmc/articles/PMC7866887/bin/peerj-09-10560-s006.xlsx Hsapiens 67 43526 43530 43710 43710 43715 43717 43526 43716 43529 43531 43531 43530 43526 43712 43718 43716 43712 43723 43718 43526 43531 43527 43530 43719 43710 43716 43717 43532 43530 43714 43525 43719 43715 43532 43529 43719 43717 43720 43527 43711 43525 43719 43714 43525 43530 43714 43714 43530 43525 43534 43712 43715 43717 43710 43714 43531 43532 43535 43533 43528 43709 43800 43710 43715 43531 43534 43533"
## [95] "PMC7859232 /pmc/articles/PMC7859232/bin/42003_2020_1469_MOESM3_ESM.xlsx Ggallus 1 43800"
## [96] "PMC7859232 /pmc/articles/PMC7859232/bin/42003_2020_1469_MOESM3_ESM.xlsx Hsapiens 15 40057 40057 40057 40057 39692 40057 39692 40057 39508 40057 36951 37500 40057 39692 37226"
## [97] "PMC7859232 /pmc/articles/PMC7859232/bin/42003_2020_1469_MOESM3_ESM.xlsx Hsapiens 14 40057 40057 40057 40057 39692 40057 39692 40057 39508 40057 36951 37500 40057 39692"
## [98] "PMC7887632 /pmc/articles/PMC7887632/bin/table1.xlsx Hsapiens 2 43892 44078"
## [99] "PMC7884756 /pmc/articles/PMC7884756/bin/Table_1.XLSX Hsapiens 2 44076 43892"
## [100] "PMC7884756 /pmc/articles/PMC7884756/bin/Table_1.XLSX Hsapiens 1 44076"
## [101] "PMC7884045 /pmc/articles/PMC7884045/bin/ACEL-20-e13293-s002.xlsx Hsapiens 19 1-Mar 10-Mar 10-Mar 7-Mar 3-Mar 11-Sep 7-Mar 4-Mar 9-Mar 1-Sep 6-Mar 9-Mar 1-Mar 1-Sep 11-Mar 1-Dec 5-Sep 11-Sep 11-Sep"
## [102] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Drerio 19 42066 42071 42069 42258 42073 42250 42278 42069 42068 42070 42064 42256 42252 42248 42067 42261 42249 42063 42069"
## [103] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Drerio 19 42066 42071 42069 42258 42073 42250 42278 42069 42068 42070 42064 42256 42252 42248 42067 42261 42249 42063 42069"
## [104] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Drerio 15 42252 42258 42248 42249 42067 42071 42066 42069 42278 42064 42070 42073 42068 42256 42261"
## [105] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Hsapiens 28 42250 42252 42251 42254 42248 42258 42250 42255 42248 42067 42249 42067 42254 42251 42253 42071 42066 42066 42069 42064 42070 42065 42063 42073 42068 42256 42253 42255"
## [106] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Drerio 16 42071 42258 42073 42069 42068 42070 42064 42256 42252 42248 42067 42261 42249 42066 42069 42278"
## [107] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Hsapiens 28 42063 42248 42254 42071 42066 42258 42073 42069 42068 42070 42064 42253 42251 42254 42256 42255 42252 42248 42067 42251 42067 42255 42253 42250 42249 42066 42250 42065"
## [108] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Drerio 16 42071 42258 42073 42069 42068 42070 42064 42256 42252 42248 42067 42261 42249 42066 42069 42278"
## [109] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Hsapiens 3 42063 42248 42254"
## [110] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Drerio 7 43345 43166 43163 43353 43167 43164 43349"
## [111] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Drerio 10 41896 41896 41896 41896 41896 41896 41896 41896 41896 41896"
## [112] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Hsapiens 39 41888 41887 41889 41892 41883 41885 41891 41893 41886 41895 41888 41887 41889 41892 41883 41885 41891 41893 41886 41895 41885 41882 41895 41887 41889 41892 41883 41891 41886 41889 41895 41887 41892 41891 41701 41890 41890 41884 41888"
## [113] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp2.xlsx Hsapiens 14 41888 41887 41889 41892 41883 41885 41891 41893 41886 41895 41882 41701 41890 41884"
## [114] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp3.xlsx Hsapiens 14 43350 43349 43351 43354 43345 43347 43353 43355 43348 43357 43344 43163 43352 43346"
## [115] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp4.xlsx Hsapiens 6 42618 42617 42622 42624 42432 42433"
## [116] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp4.xlsx Hsapiens 6 42618 42617 42622 42624 42432 42433"
## [117] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp4.xlsx Hsapiens 6 42618 42617 42622 42624 42432 42433"
## [118] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp4.xlsx Hsapiens 28 42618 42439 42617 42622 42614 42438 42430 42435 42616 42619 42627 42621 42436 42437 42434 42615 42440 42620 42431 42625 42623 42628 42430 42705 42624 42432 42433 42431"
## [119] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp4.xlsx Hsapiens 28 42618 42439 42617 42622 42614 42438 42430 42435 42616 42619 42627 42621 42436 42437 42434 42615 42440 42620 42431 42625 42623 42628 42430 42705 42624 42432 42433 42431"
## [120] "PMC7880683 /pmc/articles/PMC7880683/bin/elife-64370-supp4.xlsx Hsapiens 28 42618 42439 42617 42622 42614 42438 42430 42435 42616 42619 42627 42621 42436 42437 42434 42615 42440 42620 42431 42625 42623 42628 42430 42705 42624 42432 42433 42431"
## [121] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM11_ESM.xlsx Hsapiens 2 37316 36951"
## [122] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM15_ESM.xlsx Hsapiens 3 36951 37316 37226"
## [123] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM18_ESM.xlsx Hsapiens 2 36951 37316"
## [124] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM19_ESM.xlsx Hsapiens 3 36951 37316 37226"
## [125] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM20_ESM.xlsx Hsapiens 2 36951 37316"
## [126] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM24_ESM.xlsx Hsapiens 2 36951 36951"
## [127] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM26_ESM.xlsx Ggallus 2 37316 36951"
## [128] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM28_ESM.xlsx Hsapiens 3 37316 36951 37226"
## [129] "PMC7854732 /pmc/articles/PMC7854732/bin/41467_2020_20820_MOESM7_ESM.xlsx Hsapiens 2 36951 37316"
## [130] "PMC7882740 /pmc/articles/PMC7882740/bin/Table_3.XLSX Hsapiens 1 44077"
## [131] "PMC7851759 /pmc/articles/PMC7851759/bin/jamaneurol-e205257-s006.xlsx Hsapiens 1 43347"
## [132] "PMC7116828 /pmc/articles/PMC7116828/bin/EMS114658-supplement-Supplementary_Table_1_4.xlsx Mmusculus 5 37104 37469 37834 38200 36892"
## [133] "PMC7116828 /pmc/articles/PMC7116828/bin/EMS114658-supplement-Supplementary_Table_1_4.xlsx Mmusculus 26 37135 39326 39692 40422 38231 40603 37865 41153 38412 39508 37500 36951 39142 37681 41883 36951 38777 38047 39873 38961 40787 40057 38596 37316 40238 37316"
## [134] "PMC7851345 /pmc/articles/PMC7851345/bin/mmc2.xlsx Hsapiens 1 43892"
## [135] "PMC7851345 /pmc/articles/PMC7851345/bin/mmc2.xlsx Hsapiens 1 43892"
## [136] "PMC7851772 /pmc/articles/PMC7851772/bin/mmc2.xlsx Hsapiens 29 43161 43346 43347 43161 43350 43349 43166 43354 43168 43355 43163 43160 43165 43357 43351 43167 43345 43435 43169 43162 43344 43358 43170 43352 43348 43160 43353 43164 43344"
## [137] "PMC7875399 /pmc/articles/PMC7875399/bin/pgen.1009285.s008.xlsx Hsapiens 24 43168 43164 43167 43161 43166 43345 43165 43162 43355 43354 43353 43357 43169 43348 43352 43350 43170 43163 43346 43358 43351 43347 43349 43435"
## [138] "PMC7875399 /pmc/articles/PMC7875399/bin/pgen.1009285.s009.xlsx Hsapiens 24 43345 43353 43161 43351 43355 43358 43346 43350 43168 43357 43162 43163 43169 43170 43347 43165 43352 43166 43349 43348 43167 43164 43435 43354"
## [139] "PMC7846840 /pmc/articles/PMC7846840/bin/42003_2021_1659_MOESM4_ESM.xlsx Hsapiens 86 44076 44076 44076 44076 44076 44076 44076 44076 44076 44076 44076 44078 44078 44078 44078 44078 44078 44078 44078 44078 44078 44078 44075 44075 44075 44075 44075 44075 44075 44075 44075 44075 44075 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44081 44079 44079 44079 44079 44079 44079 44079 44079 44079 44079 44079 44080 44080 44080 44080 44080 44085 44085 44085 44085 44085 44088 44088 44088 44088 44088 44084 44084 44084 44084 44084 44082 44082 44082 44082 44082 43896 43896 43892 43892 43891 43891"
## [140] "PMC7845134 /pmc/articles/PMC7845134/bin/13059_2021_2272_MOESM10_ESM.xlsx Hsapiens 21 43892 44077 43892 44081 44080 43897 44085 43899 43894 43891 43896 44082 43898 44076 43900 43893 44083 44079 43891 44084 43895"
## [141] "PMC7845134 /pmc/articles/PMC7845134/bin/13059_2021_2272_MOESM6_ESM.xlsx Ggallus 1 43895"
## [142] "PMC7845134 /pmc/articles/PMC7845134/bin/13059_2021_2272_MOESM7_ESM.xlsx Ggallus 1 43897"
## [143] "PMC7845134 /pmc/articles/PMC7845134/bin/13059_2021_2272_MOESM8_ESM.xlsx Ggallus 1 43897"
## [144] "PMC7876278 /pmc/articles/PMC7876278/bin/Table_2.XLS Hsapiens 1 44166"
## [145] "PMC7844411 /pmc/articles/PMC7844411/bin/41467_2021_20918_MOESM5_ESM.xlsx Hsapiens 9 37681 38596 37500 36951 40787 39508 40422 37316 36951"
## [146] "PMC7844020 /pmc/articles/PMC7844020/bin/41467_2021_20892_MOESM11_ESM.xlsx Hsapiens 32 44085 43896 44083 44078 43893 44081 44081 44078 43893 44076 44082 44078 44085 44081 44081 44085 43898 43893 44078 43892 44081 44078 44085 43893 43898 43892 43893 43896 44089 43892 43893 44078"
## [147] "PMC7844020 /pmc/articles/PMC7844020/bin/41467_2021_20892_MOESM6_ESM.xlsx Hsapiens 8 43165 43354 43350 43354 43353 43354 43345 43350"
## [148] "PMC7844020 /pmc/articles/PMC7844020/bin/41467_2021_20892_MOESM6_ESM.xlsx Hsapiens 1 43354"
## [149] "PMC7844020 /pmc/articles/PMC7844020/bin/41467_2021_20892_MOESM6_ESM.xlsx Hsapiens 2 43350 43354"
## [150] "PMC7844020 /pmc/articles/PMC7844020/bin/41467_2021_20892_MOESM6_ESM.xlsx Hsapiens 1 43165"
## [151] "PMC7844020 /pmc/articles/PMC7844020/bin/41467_2021_20892_MOESM6_ESM.xlsx Hsapiens 2 43345 43350"
## [152] "PMC7844020 /pmc/articles/PMC7844020/bin/41467_2021_20892_MOESM7_ESM.xlsx Hsapiens 3 44076 44082 44085"
## [153] "PMC7873973 /pmc/articles/PMC7873973/bin/Table_1.xlsx Rnorvegicus 20 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01"
## [154] "PMC7873973 /pmc/articles/PMC7873973/bin/Table_1.xlsx Rnorvegicus 20 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01 2011-09-01"
## [155] "PMC7846933 /pmc/articles/PMC7846933/bin/mmc2.xlsx Hsapiens 2 42799 42980"
## [156] "PMC7846933 /pmc/articles/PMC7846933/bin/mmc4.xlsx Hsapiens 1 42980"
## [157] "PMC7868554 /pmc/articles/PMC7868554/bin/Table_12.XLSX Hsapiens 16 37865 38231 39326 38961 40787 41153 41883 39692 37012 37500 37226 37135 42248 40057 38596 40422"
## [158] "PMC7862794 /pmc/articles/PMC7862794/bin/Table_2.xlsx Hsapiens 1 44258"
## [159] "PMC7862768 /pmc/articles/PMC7862768/bin/Table_1.xls Hsapiens 1 43892"
## [160] "PMC7862768 /pmc/articles/PMC7862768/bin/Table_1.xls Hsapiens 4 43898 43899 43892 44166"
## [161] "PMC7862768 /pmc/articles/PMC7862768/bin/Table_1.xls Hsapiens 6 43898 43899 43892 43891 43893 44166"
## [162] "PMC7859520 /pmc/articles/PMC7859520/bin/Table_5.XLSX Drerio 1 43899"
## [163] "PMC7859435 /pmc/articles/PMC7859435/bin/Table_5.XLSX Hsapiens 101 43718 43718 43718 43718 43718 43718 43718 43718 43718 43718 43527 43527 43527 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43528 43535 43535 43535 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43530 43719 43719 43719 43719 43719 43719 43719 43719 43719 43719 43719 43526 43525 43525 43529 43534 43534 43534 43534 43534 43534 43534 43711 43720 43720 43710 43710 43714 43714 43714 43714 43714 43714 43714 43714 43714"
## [164] "PMC7880367 /pmc/articles/PMC7880367/bin/aging-13-202544-s002.xlsx Hsapiens 164 44079 44083 44083 44083 43899 44083 44083 44083 43900 44085 44083 44083 44079 43898 44083 44083 44079 44083 44083 44083 44083 43900 43900 43897 44083 44083 44085 44083 43900 44089 44083 44083 44083 44084 44083 44083 44083 44083 43893 44083 44085 44083 44083 43900 44083 43896 43900 43900 43900 43898 43896 44083 43894 44083 44083 43893 44085 43900 44083 44083 44083 44083 43900 44089 44083 44166 44083 44083 44083 43898 44083 44083 43894 44083 44085 44083 44085 44078 44081 44083 44083 44083 44083 44084 44079 44083 44083 44083 43900 44083 44083 43896 43896 43892 43891 44083 43891 44083 44083 43896 43900 44083 43898 44083 43901 44166 43900 43900 43900 44078 44085 44083 44083 44083 44083 44084 44085 43892 44086 44166 44078 43893 44077 43891 44083 43900 43900 43901 43893 43901 44166 43891 43900 43900 44085 44077 43896 43893 44078 43899 43896 43892 43896 44082 44081 44083 43900 44078 44089 44088 43899 43891 44083 44086 44089 44083 44081 43898 43898 43893 43898 43891 43891 44083"
## [165] "PMC7880367 /pmc/articles/PMC7880367/bin/aging-13-202544-s003.xlsx Hsapiens 2 43894 43901"
## [166] "PMC7880322 /pmc/articles/PMC7880322/bin/aging-13-103787-s002.xlsx Hsapiens 3 44077 44075 43894"
## [167] "PMC7845975 /pmc/articles/PMC7845975/bin/ppat.1009213.s005.xlsx Drerio 9 44080 44082 43898 43897 43892 43896 44084 44079 43894"
## [168] "PMC7845975 /pmc/articles/PMC7845975/bin/ppat.1009213.s005.xlsx Drerio 9 38961 39692 39508 39142 37316 38777 40422 38047 38596"
## [169] "PMC7845644 /pmc/articles/PMC7845644/bin/mBio.02525-20-st002.xlsx Hsapiens 4 44083 44075 44080 44080"
## [170] "PMC7848703 /pmc/articles/PMC7848703/bin/pnas.2021836118.sd04.xlsx Hsapiens 2 10-decarbamoylmitomycin C"
## [171] "PMC7848703 /pmc/articles/PMC7848703/bin/pnas.2021836118.sd05.xlsx Hsapiens 2 10-decarbamoylmitomycin C"
## [172] "PMC7848703 /pmc/articles/PMC7848703/bin/pnas.2021836118.sd07.xlsx Ggallus 2 10-decarbamoylmitomycin C"
## [173] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_2.XLSX Rnorvegicus 1 44082"
## [174] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_2.XLSX Mmusculus 1 44082"
## [175] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_2.XLSX Mmusculus 1 44078"
## [176] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_2.XLSX Rnorvegicus 1 44082"
## [177] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_3.XLSX Mmusculus 3 44083 44082 44078"
## [178] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_3.XLSX Mmusculus 1 44078"
## [179] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_3.XLSX Mmusculus 2 44085 44078"
## [180] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_3.XLSX Rnorvegicus 3 44083 44082 44078"
## [181] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_4.XLSX Mmusculus 2 44085 44082"
## [182] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_4.XLSX Mmusculus 1 44078"
## [183] "PMC7848201 /pmc/articles/PMC7848201/bin/Table_4.XLSX Mmusculus 1 44082"
## [184] "PMC7808690 /pmc/articles/PMC7808690/bin/pgen.1009302.s014.xlsx Hsapiens 1 43891"
## [185] "PMC7808690 /pmc/articles/PMC7808690/bin/pgen.1009302.s015.xlsx Hsapiens 1 43892"
## [186] "PMC7877913 /pmc/articles/PMC7877913/bin/elife-59629-supp11.xlsx Hsapiens 1 39340"
## [187] "PMC7877913 /pmc/articles/PMC7877913/bin/elife-59629-supp12.xlsx Hsapiens 1 39340"
## [188] "PMC7877913 /pmc/articles/PMC7877913/bin/elife-59629-supp12.xlsx Hsapiens 1 39340"
## [189] "PMC7877913 /pmc/articles/PMC7877913/bin/elife-59629-supp13.xlsx Hsapiens 1 39340"
## [190] "PMC7877913 /pmc/articles/PMC7877913/bin/elife-59629-supp9.xlsx Hsapiens 1 39340"
## [191] "PMC7877913 /pmc/articles/PMC7877913/bin/elife-59629-supp9.xlsx Hsapiens 1 39340"
## [192] "PMC7874222 /pmc/articles/PMC7874222/bin/Data_Sheet_2.XLSX Hsapiens 2 43712 43528"
## [193] "PMC7873862 /pmc/articles/PMC7873862/bin/Table_1.XLSX Ggallus 1 42985"
## [194] "PMC7873862 /pmc/articles/PMC7873862/bin/Table_1.XLSX Ggallus 4 42620 42617 42622 42620"
## [195] "PMC7868925 /pmc/articles/PMC7868925/bin/mmc2.xlsx Hsapiens 4 43167 43357 43169 43165"
## [196] "PMC7834956 /pmc/articles/PMC7834956/bin/Supplementary_Data4.xlsx Mmusculus 1 1-Mar"
## [197] "PMC7834956 /pmc/articles/PMC7834956/bin/Supplementary_Data5.xlsx Mmusculus 1 4-Sep"
## [198] "PMC7880379 /pmc/articles/PMC7880379/bin/aging-13-202285-s002.xlsx Hsapiens 28 43891 43894 44084 43900 44083 43899 44086 44082 44077 44078 43892 43892 44079 44085 43898 43891 44166 44076 44075 44080 43901 44081 43897 44088 43893 43896 43895 44089"
## [199] "PMC7880379 /pmc/articles/PMC7880379/bin/aging-13-202285-s003.xlsx Hsapiens 3 43891 43894 43900"
## [200] "PMC7880379 /pmc/articles/PMC7880379/bin/aging-13-202285-s006.xlsx Hsapiens 1 43900"
## [201] "PMC7880379 /pmc/articles/PMC7880379/bin/aging-13-202285-s008.xlsx Hsapiens 4 43900 43900 43900 43900"
## [202] "PMC7880379 /pmc/articles/PMC7880379/bin/aging-13-202285-s008.xlsx Hsapiens 1 43900"
## [203] "PMC7876704 /pmc/articles/PMC7876704/bin/FBA2-3-69-s001.xlsx Hsapiens 27 43892 44077 44078 43892 44081 44080 43897 44085 43899 44086 43894 43891 43896 44088 44082 43898 44076 44166 43900 43893 44075 44089 44083 44079 43891 44084 43895"
## [204] "PMC7876704 /pmc/articles/PMC7876704/bin/FBA2-3-69-s001.xlsx Hsapiens 2 44077 43894"
## [205] "PMC7834090 /pmc/articles/PMC7834090/bin/KRNB_A_1796052_SM3673.xlsx Mmusculus 1 40057"
## [206] "PMC7834090 /pmc/articles/PMC7834090/bin/KRNB_A_1796052_SM3691.xlsx Mmusculus 1 37135"
## [207] "PMC7834090 /pmc/articles/PMC7834090/bin/KRNB_A_1796052_SM3691.xlsx Mmusculus 1 38596"
## [208] "PMC7889151 /pmc/articles/PMC7889151/bin/KEPI_A_1789266_SM6918.xlsx Hsapiens 22 36951 40603 36951 40603 37316 40603 40238 37316 40603 37226 38047 37316 40238 37226 37226 37226 40238 37226 39508 37226 37226 37681"
## [209] "PMC7889151 /pmc/articles/PMC7889151/bin/KEPI_A_1789266_SM6918.xlsx Hsapiens 5 38047 37681 37681 38231 37681"
## [210] "PMC7889151 /pmc/articles/PMC7889151/bin/KEPI_A_1789266_SM6918.xlsx Hsapiens 12 37316 37316 37316 38412 38412 39508 39508 37316 40422 41153 37500 38961"
## [211] "PMC7889151 /pmc/articles/PMC7889151/bin/KEPI_A_1789266_SM6918.xlsx Hsapiens 7 37681 37681 37681 38047 40422 38231 39326"
## [212] "PMC7889151 /pmc/articles/PMC7889151/bin/KEPI_A_1789266_SM6918.xlsx Hsapiens 7 38777 39142 42248 40787 37500 37500 40057"
## [213] "PMC7889151 /pmc/articles/PMC7889151/bin/KEPI_A_1789266_SM6918.xlsx Hsapiens 15 37316 37316 37316 37681 38412 38412 39508 39508 37316 40422 41153 37500 38231 38961 39326"
## [214] "PMC7889151 /pmc/articles/PMC7889151/bin/KEPI_A_1789266_SM6918.xlsx Hsapiens 5 37681 37681 38047 38777 40422"
## [215] "PMC7889151 /pmc/articles/PMC7889151/bin/KEPI_A_1789266_SM6918.xlsx Hsapiens 6 39142 42248 40787 37500 37500 40057"
## [216] "PMC7671374 /pmc/articles/PMC7671374/bin/lqaa051_supplemental_file.xlsx Dmelanogaster 3 37226 37135 38596"
## [217] "PMC7671374 /pmc/articles/PMC7671374/bin/lqaa051_supplemental_file.xlsx Dmelanogaster 2 37500 38231"
## [218] "PMC7854777 /pmc/articles/PMC7854777/bin/NIHMS1602677-supplement-1602677_Supp_Data6.xlsx Hsapiens 1610 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 43895 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## [219] "PMC7850965 /pmc/articles/PMC7850965/bin/41380_2019_388_MOESM2_ESM.xlsx Hsapiens 1 38961"In depth look at the errors
Let’s investigate the errors in more detail.
# By species
SPECIES <- sapply(strsplit(ERROR_GENELISTS," "),"[[",3)
table(SPECIES)## SPECIES
## Athaliana Dmelanogaster Drerio Ggallus Hsapiens
## 1 6 10 12 144
## Mmusculus Rnorvegicus Scerevisiae
## 40 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##
## PMC7116828 PMC7671374 PMC7808690 PMC7834090 PMC7834956 PMC7844020 PMC7844411
## 2 2 2 3 2 7 1
## PMC7845134 PMC7845644 PMC7845975 PMC7846840 PMC7846933 PMC7848201 PMC7848703
## 4 1 2 1 2 11 3
## PMC7850965 PMC7851345 PMC7851759 PMC7851772 PMC7854732 PMC7854777 PMC7859232
## 1 2 1 1 9 1 3
## PMC7859435 PMC7859520 PMC7861375 PMC7861379 PMC7862275 PMC7862768 PMC7862794
## 1 1 3 3 1 3 1
## PMC7863008 PMC7863452 PMC7864951 PMC7865025 PMC7865055 PMC7866887 PMC7868554
## 4 1 1 3 1 2 1
## PMC7868925 PMC7870011 PMC7870932 PMC7871411 PMC7873862 PMC7873973 PMC7874222
## 1 2 2 1 2 2 1
## PMC7874467 PMC7875399 PMC7876141 PMC7876146 PMC7876278 PMC7876704 PMC7877913
## 4 2 4 1 1 2 6
## PMC7878750 PMC7880322 PMC7880367 PMC7880379 PMC7880683 PMC7880998 PMC7881037
## 1 1 2 5 19 2 5
## PMC7881115 PMC7881617 PMC7882740 PMC7884045 PMC7884410 PMC7884730 PMC7884756
## 23 1 1 1 1 1 2
## PMC7885916 PMC7887196 PMC7887632 PMC7888619 PMC7889151 PMC7890893 PMC7893110
## 6 3 1 1 8 1 1
## PMC7893923 PMC7894049 PMC7896317 PMC7896349 PMC7903802 PMC7908713
## 3 2 3 1 1 5summary(as.numeric(DIST))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.000 1.000 2.000 2.882 3.000 23.000hist(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
## 57 PMC7881115 23
## 54 PMC7880683 19
## 13 PMC7848201 11
## 19 PMC7854732 9
## 68 PMC7889151 8
## 6 PMC7844020 7
## 49 PMC7877913 6
## 64 PMC7885916 6
## 53 PMC7880379 5
## 56 PMC7881037 5
## 76 PMC7908713 5
## 8 PMC7845134 4
## 29 PMC7863008 4
## 43 PMC7874467 4
## 45 PMC7876141 4
## 4 PMC7834090 3
## 14 PMC7848703 3
## 21 PMC7859232 3
## 24 PMC7861375 3
## 25 PMC7861379 3MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES## [1] "PMC7881115"# 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## PMC7116828 PMC7671374 PMC7808690 PMC7834090 PMC7834956 PMC7844020 PMC7844411
## 31 5 2 3 2 49 9
## PMC7845134 PMC7845644 PMC7845975 PMC7846840 PMC7846933 PMC7848201 PMC7848703
## 24 4 18 86 3 17 6
## PMC7850965 PMC7851345 PMC7851759 PMC7851772 PMC7854732 PMC7854777 PMC7859232
## 1 2 1 29 21 1610 30
## PMC7859435 PMC7859520 PMC7861375 PMC7861379 PMC7862275 PMC7862768 PMC7862794
## 101 1 182 114 5 11 1
## PMC7863008 PMC7863452 PMC7864951 PMC7865025 PMC7865055 PMC7866887 PMC7868554
## 17 7 2 3 1 119 16
## PMC7868925 PMC7870011 PMC7870932 PMC7871411 PMC7873862 PMC7873973 PMC7874222
## 4 41 5 1 5 40 2
## PMC7874467 PMC7875399 PMC7876141 PMC7876146 PMC7876278 PMC7876704 PMC7877913
## 68 48 82 26 1 29 6
## PMC7878750 PMC7880322 PMC7880367 PMC7880379 PMC7880683 PMC7880998 PMC7881037
## 28 3 166 37 330 54 405
## PMC7881115 PMC7881617 PMC7882740 PMC7884045 PMC7884410 PMC7884730 PMC7884756
## 1223 3 1 19 27 27 3
## PMC7885916 PMC7887196 PMC7887632 PMC7888619 PMC7889151 PMC7890893 PMC7893110
## 801 83 2 1 79 2 7
## PMC7893923 PMC7894049 PMC7896317 PMC7896349 PMC7903802 PMC7908713
## 58 27 20 6 1 128hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
head(NERR_DF,20)## NERR
## PMC7854777 1610
## PMC7881115 1223
## PMC7885916 801
## PMC7881037 405
## PMC7880683 330
## PMC7861375 182
## PMC7880367 166
## PMC7908713 128
## PMC7866887 119
## PMC7861379 114
## PMC7859435 101
## PMC7846840 86
## PMC7887196 83
## PMC7876141 82
## PMC7889151 79
## PMC7874467 68
## PMC7893923 58
## PMC7880998 54
## PMC7844020 49
## PMC7875399 48MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR## [1] "PMC7854777"Journals affected
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
### JSON PARSING is more reliable than XML
ARTICLES <- esummary( GENELIST_ERROR_ARTICLES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA$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] 44par(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] "7881115"
##
## $result$`7881115`
## $result$`7881115`$uid
## [1] "7881115"
##
## $result$`7881115`$pubdate
## [1] "2021 Feb 12"
##
## $result$`7881115`$epubdate
## [1] "2021 Feb 12"
##
## $result$`7881115`$printpubdate
## [1] ""
##
## $result$`7881115`$source
## [1] "Nat Commun"
##
## $result$`7881115`$authors
## name authtype
## 1 Page N Author
## 2 Lemeille S Author
## 3 Vincenti I Author
## 4 Klimek B Author
## 5 Mariotte A Author
## 6 Wagner I Author
## 7 Di Liberto G Author
## 8 Kaye J Author
## 9 Merkler D Author
##
## $result$`7881115`$title
## [1] "Persistence of self-reactive CD8+ T cells in the CNS requires TOX-dependent chromatin remodeling"
##
## $result$`7881115`$volume
## [1] "12"
##
## $result$`7881115`$issue
## [1] ""
##
## $result$`7881115`$pages
## [1] "1009"
##
## $result$`7881115`$articleids
## idtype value
## 1 pmid 33579927
## 2 doi 10.1038/s41467-021-21109-3
## 3 pmcid PMC7881115
##
## $result$`7881115`$fulljournalname
## [1] "Nature Communications"
##
## $result$`7881115`$sortdate
## [1] "2021/02/12 00:00"
##
## $result$`7881115`$pmclivedate
## [1] "2021/02/25"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] "7854777"
##
## $result$`7854777`
## $result$`7854777`$uid
## [1] "7854777"
##
## $result$`7854777`$pubdate
## [1] "2020 Jul 13"
##
## $result$`7854777`$epubdate
## [1] "2020 Jul 13"
##
## $result$`7854777`$printpubdate
## [1] "2021 Jan"
##
## $result$`7854777`$source
## [1] "Nat Biotechnol"
##
## $result$`7854777`$authors
## name authtype
## 1 DeWeirdt PC Author
## 2 Sanson KR Author
## 3 Sangree AK Author
## 4 Hegde M Author
## 5 Hanna RE Author
## 6 Feeley MN Author
## 7 Griffith AL Author
## 8 Teng T Author
## 9 Borys SM Author
## 10 Strand C Author
## 11 Joung JK Author
## 12 Kleinstiver BP Author
## 13 Pan X Author
## 14 Huang A Author
## 15 Doench JG Author
##
## $result$`7854777`$title
## [1] "Optimization of AsCas12a for combinatorial genetic screens in human cells"
##
## $result$`7854777`$volume
## [1] "39"
##
## $result$`7854777`$issue
## [1] "1"
##
## $result$`7854777`$pages
## [1] "94-104"
##
## $result$`7854777`$articleids
## idtype value
## 1 pmid 32661438
## 2 doi 10.1038/s41587-020-0600-6
## 3 pmcid PMC7854777
## 4 MID NIHMS1602677
##
## $result$`7854777`$fulljournalname
## [1] "Nature biotechnology"
##
## $result$`7854777`$sortdate
## [1] "2020/07/13 00:00"
##
## $result$`7854777`$pmclivedate
## [1] "2021/02/03"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 3.6.3 (2020-02-29)
## 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
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.6 knitr_1.31 magrittr_2.0.1 R6_2.5.0
## [5] rlang_0.4.10 highr_0.8 stringr_1.4.0 tools_3.6.3
## [9] xfun_0.22 jquerylib_0.1.3 htmltools_0.5.1.1 yaml_2.2.1
## [13] digest_0.6.27 assertthat_0.2.1 sass_0.3.1 bitops_1.0-6
## [17] RCurl_1.98-1.3 evaluate_0.14 rmarkdown_2.7 stringi_1.5.3
## [21] compiler_3.6.3 bslib_0.2.4 cellranger_1.1.0 XML_3.99-0.3