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 @@
 <P>
 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. 
 <div> <img border=1 src='/images/gtex/gtexSampleRin.V6.png'></div>
 <p></p>
 <div><img border=1 src='/images/gtex/gtexSampleAge.V6.png'></div></p>
 <p>
 Additional summary plots of GTEx sample characteristics are available at the 
 <a target="_blank" href="https://gtexportal.org/home/tissueSummaryPage">
 GTEx Portal Tissue Summary</a> page.</p>
 
+
 <h2>Data Access</h2>
 <p>
-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 
 <a href="hgTables?db=$db&hgta_track=$db&hgta_group=allTables&hgta_table=gtexGene">
-gtexGene table</a>. Supplementary information can be found in the connected tables below.
+Table Browser</a> or <a href="hgIntegrator">Data Integrator</a>. Metadata can be 
+found in the connected tables below.
 <ul>
-<li><strong><a href="hgTables?db=$db&hgta_track=hgFixed&hgta_group=allTables&hgta_table=hgFixed.gtexTissue">
-gtexTissue</a></strong> has information on the order of each of the 53 tissues in the expression
-data.</li>
-<li><strong><a href="hgTables?db=$db&hgta_track=$db&hgta_group=allTables&hgta_table=gtexGeneModel">
-gtexGeneModel</a></strong> describes the gene names and coordinates.</li> 
-<li><strong><a href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexSampleData">
-gtexSampleData</a></strong> has scores for each individual gene-sample data point.</li>
-<li><strong><a href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexSample">
-gtexSample</a></strong> contains metadata about sample isolation time, collection site, and tissue notes.</li>
-<li><strong><a href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexDonor">
-gtexDonor</a></strong> has anonymized information on the tissue donor.</li></ul></p>
+<li><strong><a 
+href="hgTables?db=$db&hgta_track=$db&hgta_group=allTables&hgta_table=gtexGeneModel">
+gtexGeneModel</a></strong> describes the gene names and coordinates in genePred format.</li> 
+<li><strong><a 
+href="hgTables?db=$db&hgta_track=hgFixed&hgta_group=allTables&hgta_table=hgFixed.gtexTissue">
+hgFixed.gtexTissue</a></strong> lists each of the 53 tissues in alphabetical order,
+corresponding to the comma separated expression values in gtexGene.</li>
+<li><strong><a 
+href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexSampleData">
+hgFixed.gtexSampleData</a></strong> has RPKM expression scores for each individual gene-sample 
+data point, connected to gtexSample.</li>
+<li><strong><a 
+href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexSample">
+hgFixed.gtexSample</a></strong> contains metadata about sample time, collection site,
+and tissue, connected to the donor field in the gtexDonor table.</li>
+<li><strong><a 
+href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexDonor">
+hgFixed.gtexDonor</a></strong> has anonymized information on the tissue donor.</li></ul></p>
+<p>
+For automated analysis and downloads, the track data files can be downloaded from 
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/gtex/">our downloads server</a>
+or <a href="../goldenPath/help/api.html">the JSON API</a>.
+Individual regions or the whole genome annotation can be accessed as text using our utility
+<code>bigBedToBed</code>. Instructions for downloading the utility can be found 
+<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. 
+That utility can also be used to obtain features within a given range, e.g. 
+<code>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/gtex/gtexTranscExpr.bb -chrom=chr21
+-start=0 -end=100000000 stdout</code></p>
 <p>
 Data can also be obtained directly from GTEx at the following link:
 <a href="https://gtexportal.org/home/datasets" target=_blank>
 https://gtexportal.org/home/datasets</a></p>
 
 <H2>Credits</H2>
 <P>
 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.</P>
 
 <H2>References</H2>
 <p>
 GTEx Consortium.
 <a href="https://www.nature.com/ng/journal/v45/n6/full/ng.2653.html" target="_blank">