5de72d67529fe096500e1009c53a83afaec25b96 kate Mon Apr 27 18:26:26 2020 -0700 Update GTEx Gene track description for V8. refs #25130 diff --git src/hg/makeDb/trackDb/human/gtexGeneV8.html src/hg/makeDb/trackDb/human/gtexGeneV8.html new file mode 100644 index 0000000..901a6d3 --- /dev/null +++ src/hg/makeDb/trackDb/human/gtexGeneV8.html @@ -0,0 +1,176 @@ +<H2>Description</H2> +<P> +The +<a target="_blank" href="https://commonfund.nih.gov/GTEx/index">NIH Genotype-Tissue Expression (GTEx) project</a> +was created to establish a sample and data resource for studies on the relationship between +genetic variation and gene expression in multiple human tissues. +This track shows median gene expression levels in 52 tissues and 2 cell lines, +based on RNA-seq data from the GTEx final data release (V8, August 2019). +This release is based on data from 17382 tissue samples obtained from 948 adult post-mortem individuals.</P> + +<H2>Display Conventions</H2> +<P> +In Full and Pack display modes, expression for each gene is represented by a colored bargraph, +where the height of each bar represents the median expression level across all samples for a +tissue, and the bar color indicates the tissue. +Tissue colors were assigned to conform to the GTEx Consortium publication conventions. +<br> <img border='1' src="../images/gtex/gtexGeneTcap.png"><br> +The bargraph display has the same width and tissue order for all genes. +Mouse hover over a bar will show the tissue and median expression level. +The Squish display mode draws a rectangle for each gene, colored to indicate the tissue +with highest expression level if it contributes more than 10% to the overall expression +(and colored black if no tissue predominates). +In Dense mode, the darkness of the grayscale rectangle displayed for the gene reflects the total +median expression level across all tissues.</p> +<p> +The GTEx transcript model used to quantify expression level is displayed below the graph, +colored to indicate the transcript class +(<span style='color: #0c0c78'>coding</span>, +<span style='color: #006400'>noncoding</span>, +<span style='color: #FF33FF'>pseudogene</span>, +<span style='color: #FE0000'>problem</span>), +following GENCODE conventions. +</p> +<P> +Click-through on a graph displays a boxplot of expression level quartiles with outliers, +per tissue, along with a link to the corresponding gene page on the GTEx Portal.</P> +The track configuration page provides controls to limit the genes and tissues displayed, +and to select raw or log transformed expression level display.</P> + +<H2>Methods</H2> +Tissue samples were obtained using the GTEx standard operating procedures for informed consent +and tissue collection, in conjunction with the +<a target="_blank" href="https://biospecimens.cancer.gov/resources/sops/gtex.asp"> +National Cancer Institute Biorepositories and Biospecimen</a>. +All tissue specimens were reviewed by pathologists to characterize and +verify organ source. +Images from stained tissue samples can be viewed via the +<a target="_blank" href="https://brd.nci.nih.gov/brd/image-search/searchhome"> +NCI histopathology viewer</a>. +The Qiagen PAXgene non-formalin tissue preservation product was used to stabilize +tissue specimens without cross-linking biomolecules.</P> +<P> +RNA-seq was performed by the GTEx Laboratory, Data Analysis and Coordinating Center +(LDACC) at the Broad Institute. +The Illumina TruSeq protocol was used to create an unstranded polyA+ library sequenced +on the Illumina HiSeq 2000 and HiSeq 2500 platforms to produce 76-bp paired end reads with a coverage +goal of 50M (median achieved was ~82M total reads). +</P> +Sequence reads were aligned to the hg38/GRCh38 human genome using STAR v2.5.3a +assisted by the GENCODE 26 transcriptome definition. +The alignment pipeline is available +<a target="_blank" href="https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq">here</a>. +</p> +<a> +Gene annotations were produced using a custom isoform collapsing procedure that excluded +retained intron and read through transcripts, merged overlapping exon intervals and then excluded +exon intervals overlapping between genes. +Gene expression levels in TPM were called via the RNA-SeQC tool (v1.1.9), after filtering for +unique mapping, proper pairing, and exon overlap. +For further method details, see the +<a target="_blank" href="https://gtexportal.org/home/documentationPage#staticTexAnalysisMethods"> +GTEx Portal Documentation</a> page. +<P> +UCSC obtained the gene-level expression files, gene annotations and sample metadata from the +GTEx Portal Download page. +Median expression level in TPM was computed per gene/per tissue.</P> + +<H2>Subject and Sample Characteristics</H2> +<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> +--> +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> +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=gtexGeneV8"> +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=$db&hgta_track=$db&hgta_group=allTables&hgta_table=gtexGeneModelV8"> +gtexGeneModelV8</a></strong> describes the gene names and coordinates in genePred format.</li> +<li><strong><a +href="hgTables?db=$db&hgta_track=hgFixed&hgta_group=allTables&hgta_table=hgFixed.gtexTissueV8"> +hgFixed.gtexTissueV8</a></strong> lists each of the 53 tissues in alphabetical order, +corresponding to the comma separated expression values in gtexGeneV8.</li> +<li><strong><a +href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexSampleDataV8"> +hgFixed.gtexSampleDataV8</a></strong> has TPM expression scores for each individual gene-sample +data point, connected to gtexSampleV8.</li> +<li><strong><a +href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexSampleV8"> +hgFixed.gtexSampleV8</a></strong> contains metadata about sample time, collection site, +and tissue, connected to the donor field in the gtexDonorV8 table.</li> +<li><strong><a +href="hgTables?db=$db&hgta_group=allTables&hgta_track=hgFixed&hgta_table=hgFixed.gtexDonorV8"> +hgFixed.gtexDonorV8</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/hg38/gtex/gtexGeneV8.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"> +The Genotype-Tissue Expression (GTEx) project</a>. +<em>Nat Genet</em>. 2013 Jun;45(6):580-5. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23715323" target="_blank">23715323</a>; +PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010069/" target="_blank">PMC4010069</a> </p> + +<p> +Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/26484571/" target="_blank"> +A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project</a>. +<em>Biopreserv Biobank</em>. 2015 Oct;13(5):311-9. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26484571" target="_blank">26484571</a>; +PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675181/" target="_blank">PMC4675181</a></p> + +Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, +Pervouchine DD, Sullivan TJ <em>et al</em>. +<a href="https://science.sciencemag.org/content/348/6235/660" target="_blank"> +Human genomics. The human transcriptome across tissues and individuals</a>. +<em>Science</em>. 2015 May 8;348(6235):660-5. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25954002" target="_blank">25954002</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547472/" target="_blank">PMC4547472</a></p> + +<p> +DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. +<a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts196" +target="_blank"> +RNA-SeQC: RNA-seq metrics for quality control and process optimization</a>. +<em>Bioinformatics</em>. 2012 Jun 1;28(11):1530-2. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22539670" target="_blank">22539670</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356847/" target="_blank">PMC3356847</a></p> +