GTEx Gene V8 Track Settings
 
Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019)   (All Expression tracks)

Display mode:   

Show only items with score at or above:   (range: 0 to 1000)

Label:  gene symbol  accession  both 
Limit to protein-coding genes:    Show GTEx gene model:
Log10 transform:    View limits maximum: TPM (range 0-747400)

Tissues:  
        Tissue Samples Organ System
 Adipose - Subcutaneous  663  Adipose Tissue  Other
 Adipose - Visceral (Omentum)  541  Adipose Tissue  Other
 Adrenal Gland  258  Adrenal Gland  Endocrine
 Artery - Aorta  432  Blood Vessel  Cardiovascular
 Artery - Coronary  240  Blood Vessel  Cardiovascular
 Artery - Tibial  663  Blood Vessel  Cardiovascular
 Bladder  21  Bladder  Other
 Brain - Amygdala  152  Brain  Brain
 Brain - Anterior cingulate cortex (BA24)  176  Brain  Brain
 Brain - Caudate (basal ganglia)  246  Brain  Brain
 Brain - Cerebellar Hemisphere  215  Brain  Brain
 Brain - Cerebellum  241  Brain  Brain
 Brain - Cortex  255  Brain  Brain
 Brain - Frontal Cortex (BA9)  209  Brain  Brain
 Brain - Hippocampus  197  Brain  Brain
 Brain - Hypothalamus  202  Brain  Brain
 Brain - Nucleus accumbens (basal ganglia)  246  Brain  Brain
 Brain - Putamen (basal ganglia)  205  Brain  Brain
 Brain - Spinal cord (cervical c-1)  159  Brain  Brain
 Brain - Substantia nigra  139  Brain  Brain
 Breast - Mammary Tissue  459  Breast  Reproductive
 Cells - EBV-transformed lymphocytes  174  Blood  Other
 Cells - Cultured fibroblasts  0  Skin  Other
 Cervix - Ectocervix  9  Cervix Uteri  Reproductive
 Cervix - Endocervix  10  Cervix Uteri  Reproductive
 Colon - Sigmoid  373  Colon  Digestive
 Colon - Transverse  406  Colon  Digestive
 Esophagus - Gastroesophageal Junction  375  Esophagus  Digestive
 Esophagus - Mucosa  555  Esophagus  Digestive
 Esophagus - Muscularis  515  Esophagus  Digestive
 Fallopian Tube  9  Fallopian Tube  Reproductive
 Heart - Atrial Appendage  429  Heart  Cardiovascular
 Heart - Left Ventricle  432  Heart  Cardiovascular
 Kidney - Cortex  85  Kidney  Other
 Kidney - Medulla  4  Kidney - Medulla  Other
 Liver  226  Liver  Digestive
 Lung  578  Lung  Other
 Minor Salivary Gland  162  Salivary Gland  Other
 Muscle - Skeletal  803  Muscle  Other
 Nerve - Tibial  619  Nerve  Other
 Ovary  180  Ovary  Reproductive
 Pancreas  328  Pancreas  Digestive
 Pituitary  283  Pituitary  Endocrine
 Prostate  245  Prostate  Reproductive
 Skin - Not Sun Exposed (Suprapubic)  604  Skin  Other
 Skin - Sun Exposed (Lower leg)  701  Skin  Other
 Small Intestine - Terminal Ileum  187  Small Intestine  Digestive
 Spleen  241  Spleen  Other
 Stomach  359  Stomach  Digestive
 Testis  361  Testis  Reproductive
 Thyroid  653  Thyroid  Endocrine
 Uterus  142  Uterus  Reproductive
 Vagina  156  Vagina  Reproductive
 Whole Blood  755  Blood  Other
View table schema
Data last updated: 2020-04-28


new Note: Released May. 22, 2020

Description

The NIH Genotype-Tissue Expression (GTEx) project 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 17,382 tissue samples obtained from 948 adult post-mortem individuals.

Display Conventions

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.
     
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.

The GTEx transcript model used to quantify expression level is displayed below the graph, colored to indicate the transcript class (coding, noncoding, pseudogene, problem), following GENCODE conventions.

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.

The track configuration page provides controls to limit the genes and tissues displayed, and to select raw or log transformed expression level display.

Methods

Tissue samples were obtained using the GTEx standard operating procedures for informed consent and tissue collection, in conjunction with the National Cancer Institute Biorepositories and Biospecimen. All tissue specimens were reviewed by pathologists to characterize and verify organ source. Images from stained tissue samples can be viewed via the NCI histopathology viewer. The Qiagen PAXgene non-formalin tissue preservation product was used to stabilize tissue specimens without cross-linking biomolecules.

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).

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 here.

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 GTEx Portal Documentation page.

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.

Subject and Sample Characteristics

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

Data Access

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

  • gtexGeneModelV8 describes the gene names and coordinates in genePred format.
  • hgFixed.gtexTissueV8 lists each of the 53 tissues in alphabetical order, corresponding to the comma separated expression values in gtexGeneV8.
  • hgFixed.gtexSampleDataV8 has TPM expression scores for each individual gene-sample data point, connected to gtexSampleV8.
  • hgFixed.gtexSampleV8 contains metadata about sample time, collection site, and tissue, connected to the donor field in the gtexDonorV8 table.
  • hgFixed.gtexDonorV8 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/hg38/gtex/gtexGeneV8.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. The GTEx Consortium atlas of genetic regulatory effects across human tissues. In press.

GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. PMID: 23715323; PMC: PMC4010069

Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreserv Biobank. 2015 Oct;13(5):311-9. PMID: 26484571; PMC: PMC4675181

Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ et al. Human genomics. The human transcriptome across tissues and individuals. Science. 2015 May 8;348(6235):660-5. PMID: 25954002; PMC: PMC4547472

DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012 Jun 1;28(11):1530-2. PMID: 22539670; PMC: PMC3356847