GTEx data into Bgee

In addition to the continuous growth of transcriptomics datasets, some specific projects produce large amounts of data, generated and accessible in a consistent manner, as, notably, the GTEx project. The GTEx project aims at building a comprehensive resource for tissue-specific gene expression in human. Here we describe how this dataset was integrated into Bgee.

Annotation process

We applied a stringent re-annotation process to the GTEx data to retain only healthy tissues and non-contaminated samples, using the information available under restricted-access. For instance, we rejected all samples for 31% of subjects, deemed globally unhealthy from the pathology report (e.g., drug abuse, diabetes, BMI > 35), as well as specific samples from another 28% of subjects who had local pathologies (e.g., brain from Alzheimer patients). We also rejected samples with contamination from other tissues.

In total, only 50% of samples were kept; these represent a high quality subset of GTEx. All these samples were re-annotated manually to specific Uberon anatomy and aging terms.

GTEx data into Bgee

All corresponding RNA-seq were reanalyzed in the Bgee pipeline, consistently with all other healthy RNA-seq from human and other species. These data are being made available both through the website, and through BgeeDB R package (with sensitive information hidden).

GTEx data into our website

  • Annotations can be retrieved from RNA-Seq human experiments/libraries info. Experiment ID of GTEx is 'SRP012682'.
  • Processed expression values, from GTEx only, are available on our FTP (download file).
  • Gene expression calls are included into human files
  • Each human gene page includes GTEx data if there is any (search a gene here).
  • TopAnat analyses can be performs here, which leverage the power of the abundant GTEx data integrated with many smaller datasets to provide biological insight into gene lists.

GTEx data using BgeeDB R package

More information and examples can be found on the BgeeDB R package page.

  • Annotations can be retrieved from RNA-Seq human experiments/libraries information. Experiment ID of GTEx is 'SRP012682'.
        source("https://bioconductor.org/biocLite.R")
        biocLite("BgeeDB")
        library(BgeeDB)
        bgee <- Bgee$new(species = "Homo_sapiens", dataType = "rna_seq")
        myAnnotation <- getAnnotation(bgee)
    
  • Quantitative expression data and presence calls for GTEx can be loaded.
        bgee <- Bgee$new(species = "Homo_sapiens", dataType = "rna_seq")
        # This step can take a lot of time as all Bgee GTEx data have to be downloaded and uncompressed.
        dataGTEx <- getData(bgee, experimentId = "SRP012682")
    
  • TopAnat analyses can be performs, which leverage the power of the abundant GTEx data integrated with many smaller datasets to provide biological insight into gene lists.
        bgee <- Bgee$new(species = "Homo_sapiens")
        myTopAnatData <- loadTopAnatData(bgee)
        # Retrieve all genes with data in Bgee
        allGenes <- unique(row.names(myTopAnatData$gene2anatomy))
        # List of genes related to autism and epilepsy from Jabbari 2016
        genesOfInterest <- c("ENSG00000183044", "ENSG00000085563", "ENSG00000006071", "ENSG00000153086", 
        "ENSG00000243989", "ENSG00000156110", "ENSG00000150594", "ENSG00000239900", 
        "ENSG00000141385", "ENSG00000038002", "ENSG00000142208", "ENSG00000275199", 
        "ENSG00000117020", "ENSG00000163631", "ENSG00000159423", "ENSG00000112294", 
        "ENSG00000164904", "ENSG00000033011", "ENSG00000182858", "ENSG00000101901", 
        "ENSG00000119523", "ENSG00000214160", "ENSG00000088035", "ENSG00000159063", 
        "ENSG00000086848", "ENSG00000242110", "ENSG00000137074", "ENSG00000124198", 
        "ENSG00000118520", "ENSG00000198844", "ENSG00000131089", "ENSG00000100299", 
        "ENSG00000113273", "ENSG00000004848", "ENSG00000104763", "ENSG00000108381", 
        "ENSG00000066279", "ENSG00000138363", "ENSG00000159363", "ENSG00000018625", 
        "ENSG00000174437", "ENSG00000182220", "ENSG00000185344", "ENSG00000171953", 
        "ENSG00000175054", "ENSG00000158321", "ENSG00000086062", "ENSG00000103507", 
        "ENSG00000074582", "ENSG00000176697", "ENSG00000157764", "ENSG00000106009", 
        "ENSG00000164061", "ENSG00000169814", "ENSG00000111678", "ENSG00000130921", 
        "ENSG00000131943", "ENSG00000197603", "ENSG00000141837", "ENSG00000007402", 
        "ENSG00000182389", "ENSG00000198668", "ENSG00000143933", "ENSG00000147044", 
        "ENSG00000036828", "ENSG00000110395", "ENSG00000015133", "ENSG00000108691", 
        "ENSG00000136861", "ENSG00000008086", "ENSG00000064309", "ENSG00000151849", 
        "ENSG00000103995", "ENSG00000173575", "ENSG00000100888", "ENSG00000168539", 
        "ENSG00000181072", "ENSG00000120903", "ENSG00000101204", "ENSG00000175344", 
        "ENSG00000274542", "ENSG00000160716", "ENSG00000114859", "ENSG00000073464", 
        "ENSG00000186510", "ENSG00000184908", "ENSG00000188603", "ENSG00000102805", 
        "ENSG00000128973", "ENSG00000182372", "ENSG00000278220", "ENSG00000184144", 
        "ENSG00000278728", "ENSG00000174469", "ENSG00000166685", "ENSG00000168434", 
        "ENSG00000213380", "ENSG00000142173", "ENSG00000173085", "ENSG00000088682", 
        "ENSG00000006695", "ENSG00000014919", "ENSG00000047457", "ENSG00000165078", 
        "ENSG00000157184", "ENSG00000169372", "ENSG00000147571", "ENSG00000160213", 
        "ENSG00000064601", "ENSG00000117984", "ENSG00000174080", "ENSG00000115827", 
        "ENSG00000077279", "ENSG00000100150", "ENSG00000181192", "ENSG00000091140", 
        "ENSG00000101152", "ENSG00000116675", "ENSG00000116641", "ENSG00000172269", 
        "ENSG00000000419", "ENSG00000136908", "ENSG00000179085", "ENSG00000188641", 
        "ENSG00000197102", "ENSG00000157540", "ENSG00000101210", "ENSG00000096093", 
        "ENSG00000111361", "ENSG00000119718", "ENSG00000070785", "ENSG00000115211", 
        "ENSG00000145191", "ENSG00000170370", "ENSG00000133216", "ENSG00000112425", 
        "ENSG00000178607", "ENSG00000140374", "ENSG00000105379", "ENSG00000171503", 
        "ENSG00000103089", "ENSG00000122591", "ENSG00000145982", "ENSG00000091483", 
        "ENSG00000112367", "ENSG00000196924", "ENSG00000162769", "ENSG00000119686", 
        "ENSG00000110195", "ENSG00000170345", "ENSG00000125740", "ENSG00000176165", 
        "ENSG00000160973", "ENSG00000087086", "ENSG00000179163", "ENSG00000022355", 
        "ENSG00000166206", "ENSG00000187730", "ENSG00000113327", "ENSG00000054983", 
        "ENSG00000141012", "ENSG00000130005", "ENSG00000171766", "ENSG00000105607", 
        "ENSG00000140905", "ENSG00000131095", "ENSG00000170266", "ENSG00000178445", 
        "ENSG00000074047", "ENSG00000145888", "ENSG00000109738", "ENSG00000173540", 
        "ENSG00000087258", "ENSG00000159921", "ENSG00000111670", "ENSG00000090581", 
        "ENSG00000135677", "ENSG00000108433", "ENSG00000171723", "ENSG00000233276", 
        "ENSG00000176884", "ENSG00000183454", "ENSG00000273079", "ENSG00000152822", 
        "ENSG00000169919", "ENSG00000138796", "ENSG00000170445", "ENSG00000172534", 
        "ENSG00000164588", "ENSG00000138622", "ENSG00000213614", "ENSG00000049860", 
        "ENSG00000165102", "ENSG00000153187", "ENSG00000158104", "ENSG00000174775", 
        "ENSG00000276536", "ENSG00000072506", "ENSG00000114378", "ENSG00000181873", 
        "ENSG00000010404", "ENSG00000127415", "ENSG00000134049", "ENSG00000166333", 
        "ENSG00000124313", "ENSG00000150995", "ENSG00000120071", "ENSG00000278458", 
        "ENSG00000275867", "ENSG00000111262", "ENSG00000169282", "ENSG00000069424", 
        "ENSG00000184408", "ENSG00000140015", "ENSG00000151704", "ENSG00000177807", 
        "ENSG00000187486", "ENSG00000156113", "ENSG00000281151", "ENSG00000075043", 
        "ENSG00000184156", "ENSG00000107147", "ENSG00000243335", "ENSG00000068796", 
        "ENSG00000276734", "ENSG00000168280", "ENSG00000185467", "ENSG00000118162", 
        "ENSG00000133703", "ENSG00000087299", "ENSG00000196569", "ENSG00000143815", 
        "ENSG00000108231", "ENSG00000121897", "ENSG00000138095", "ENSG00000187391", 
        "ENSG00000169032", "ENSG00000126934", "ENSG00000109339", "ENSG00000204406", 
        "ENSG00000090674", "ENSG00000147316", "ENSG00000169057", "ENSG00000081189", 
        "ENSG00000164073", "ENSG00000168282", "ENSG00000100427", "ENSG00000124615", 
        "ENSG00000164172", "ENSG00000129255", "ENSG00000178802", "ENSG00000177000", 
        "ENSG00000198793", "ENSG00000196091", "ENSG00000108784", "ENSG00000072864", 
        "ENSG00000275911", "ENSG00000125356", "ENSG00000131495", "ENSG00000023228", 
        "ENSG00000213619", "ENSG00000164258", "ENSG00000115286", "ENSG00000110717", 
        "ENSG00000167792", "ENSG00000049759", "ENSG00000223957", "ENSG00000204386", 
        "ENSG00000234343", "ENSG00000228691", "ENSG00000227129", "ENSG00000184494", 
        "ENSG00000227315", "ENSG00000234846", "ENSG00000196712", "ENSG00000151092", 
        "ENSG00000187566", "ENSG00000087303", "ENSG00000164190", "ENSG00000156574", 
        "ENSG00000074181", "ENSG00000141458", "ENSG00000119655", "ENSG00000122585", 
        "ENSG00000185149", "ENSG00000213281", "ENSG00000179915", "ENSG00000079482", 
        "ENSG00000116329", "ENSG00000112038", "ENSG00000187848", "ENSG00000135124", 
        "ENSG00000007168", "ENSG00000125779", "ENSG00000173599", "ENSG00000165194", 
        "ENSG00000160299", "ENSG00000131828", "ENSG00000148459", "ENSG00000164494", 
        "ENSG00000127980", "ENSG00000108733", "ENSG00000142655", "ENSG00000121680", 
        "ENSG00000164751", "ENSG00000215193", "ENSG00000034693", "ENSG00000139197", 
        "ENSG00000124587", "ENSG00000112357", "ENSG00000102144", "ENSG00000156531", 
        "ENSG00000092621", "ENSG00000165195", "ENSG00000108474", "ENSG00000165282", 
        "ENSG00000124155", "ENSG00000060642", "ENSG00000121879", "ENSG00000184381", 
        "ENSG00000182621", "ENSG00000123560", "ENSG00000140650", "ENSG00000039650", 
        "ENSG00000108439", "ENSG00000140521", "ENSG00000115138", "ENSG00000131238", 
        "ENSG00000102103", "ENSG00000139174", "ENSG00000163637", "ENSG00000100033", 
        "ENSG00000167371", "ENSG00000197746", "ENSG00000185920", "ENSG00000179295", 
        "ENSG00000172053", "ENSG00000151552", "ENSG00000155961", "ENSG00000132155", 
        "ENSG00000108557", "ENSG00000146282", "ENSG00000078328", "ENSG00000167281", 
        "ENSG00000189056", "ENSG00000163933", "ENSG00000155906", "ENSG00000104889", 
        "ENSG00000136104", "ENSG00000172922", "ENSG00000067836", "ENSG00000151835", 
        "ENSG00000101347", "ENSG00000138760", "ENSG00000144285", "ENSG00000105711", 
        "ENSG00000136531", "ENSG00000153253", "ENSG00000183873", "ENSG00000196876", 
        "ENSG00000169432", "ENSG00000130489", "ENSG00000073578", "ENSG00000178980", 
        "ENSG00000152217", "ENSG00000127990", "ENSG00000181523", "ENSG00000164690", 
        "ENSG00000108061", "ENSG00000138083", "ENSG00000064651", "ENSG00000124140", 
        "ENSG00000119899", "ENSG00000135917", "ENSG00000106688", "ENSG00000110436", 
        "ENSG00000079215", "ENSG00000102743", "ENSG00000125454", "ENSG00000177542", 
        "ENSG00000117394", "ENSG00000164414", "ENSG00000117620", "ENSG00000181830", 
        "ENSG00000076351", "ENSG00000144290", "ENSG00000142319", "ENSG00000276996", 
        "ENSG00000165970", "ENSG00000130821", "ENSG00000198689", "ENSG00000072501", 
        "ENSG00000108055", "ENSG00000166311", "ENSG00000102172", "ENSG00000163877", 
        "ENSG00000115904", "ENSG00000104450", "ENSG00000152583", "ENSG00000166068", 
        "ENSG00000197694", "ENSG00000102359", "ENSG00000126091", "ENSG00000115525", 
        "ENSG00000124356", "ENSG00000123473", "ENSG00000136854", "ENSG00000144455", 
        "ENSG00000139531", "ENSG00000148290", "ENSG00000008056", "ENSG00000197283", 
        "ENSG00000227460", "ENSG00000102003", "ENSG00000198198", "ENSG00000164458", 
        "ENSG00000136463", "ENSG00000143374", "ENSG00000054611", "ENSG00000162065", 
        "ENSG00000145979", "ENSG00000184058", "ENSG00000143178", "ENSG00000196628", 
        "ENSG00000177426", "ENSG00000175606", "ENSG00000061938", "ENSG00000166340", 
        "ENSG00000213689", "ENSG00000165699", "ENSG00000103197", "ENSG00000154743", 
        "ENSG00000274672", "ENSG00000275165", "ENSG00000274796", "ENSG00000274078", 
        "ENSG00000278712", "ENSG00000273896", "ENSG00000170892", "ENSG00000274129", 
        "ENSG00000278605", "ENSG00000278622", "ENSG00000182173", "ENSG00000175894", 
        "ENSG00000104833", "ENSG00000131462", "ENSG00000128159", "ENSG00000198431", 
        "ENSG00000114062", "ENSG00000104517", "ENSG00000173218", "ENSG00000137411", 
        "ENSG00000236178", "ENSG00000234032", "ENSG00000206476", "ENSG00000230985", 
        "ENSG00000223494", "ENSG00000213585", "ENSG00000165637", "ENSG00000197969", 
        "ENSG00000141252", "ENSG00000196998", "ENSG00000075702", "ENSG00000186153", 
        "ENSG00000169554", "ENSG00000043355")
        # Build the gene vector for the analysis
        geneList <- factor(as.integer(unique(allGenes) %in% genesOfInterest))
        names(geneList) <- unique(allGenes)
        # Run the test
        myTopAnatObject <- topAnat(myTopAnatData, geneList)
        resFis <- runTest(myTopAnatObject, algorithm ="elim", statistic ="fisher")
        # Format results
        tableOver <- makeTable(myTopAnatData, myTopAnatObject, resFis, 0.1)
        tableOver
    

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