51bc9725be0e2110befd07389bf7287f0ce7c256 dschmelt Fri Jan 24 17:10:07 2020 -0800 Adding more info to the Data Access section to GTEx page refs #24826 diff --git src/hg/makeDb/trackDb/human/gtexGeneExpr.html src/hg/makeDb/trackDb/human/gtexGeneExpr.html index af9cfc7..3e40410 100644 --- src/hg/makeDb/trackDb/human/gtexGeneExpr.html +++ src/hg/makeDb/trackDb/human/gtexGeneExpr.html @@ -72,47 +72,66 @@

The scientific goal of the GTEx project required that the donors and their biospecimen present with no evidence of disease. The tissue types collected were chosen based on their clinical significance, logistical feasibility and their relevance to the scientific goal of the project and the research community. Postmortem samples were collected from non-diseased donors with ages ranging from 20 to 79. 34.4% of donors were female and 65.6% male.

Additional summary plots of GTEx sample characteristics are available at the GTEx Portal Tissue Summary page.

+

Data Access

-GTEx Gene expression data can be accessed through the Table Browser in the +The raw data for the GTEx Gene expression track can be accessed interactively through the -gtexGene table. Supplementary information can be found in the connected tables below. +Table Browser or Data Integrator. Metadata can be +found in the connected tables below.

+
  • +gtexGeneModel describes the gene names and coordinates in genePred format.
    • +
  • +hgFixed.gtexTissue lists each of the 53 tissues in alphabetical order, +corresponding to the comma separated expression values in gtexGene.
    • +
  • +hgFixed.gtexSampleData has RPKM expression scores for each individual gene-sample +data point, connected to gtexSample.
    • +
  • +hgFixed.gtexSample contains metadata about sample time, collection site, +and tissue, connected to the donor field in the gtexDonor table.
    • +
  • +hgFixed.gtexDonor has anonymized information on the tissue donor.

    • +

    +For automated analysis and downloads, the track data files can be downloaded from +our downloads server +or the JSON API. +Individual regions or the whole genome annotation can be accessed as text using our utility +bigBedToBed. Instructions for downloading the utility can be found +here. +That utility can also be used to obtain features within a given range, e.g. +bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/gtex/gtexTranscExpr.bb -chrom=chr21 +-start=0 -end=100000000 stdout

    Data can also be obtained directly from GTEx at the following link: https://gtexportal.org/home/datasets

    Credits

    Statistical analysis and data interpretation was performed by The GTEx Consortium Analysis Working Group. Data was provided by the GTEx LDACC at The Broad Institute of MIT and Harvard.

    References

    GTEx Consortium.