GTEx Gene Track Settings
 
Gene Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors)   (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: RPKM (range 0-711778)

Tissues:  
        Tissue Samples Organ System
 Adipose - Subcutaneous  350  Adipose Tissue  Other
 Adipose - Visceral (Omentum)  227  Adipose Tissue  Other
 Adrenal Gland  145  Adrenal Gland  Endocrine
 Artery - Aorta  224  Blood Vessel  Cardiovascular
 Artery - Coronary  133  Blood Vessel  Cardiovascular
 Artery - Tibial  332  Blood Vessel  Cardiovascular
 Bladder  11  Bladder  Other
 Brain - Amygdala  72  Brain  Brain
 Brain - Anterior cingulate cortex (BA24)  84  Brain  Brain
 Brain - Caudate (basal ganglia)  117  Brain  Brain
 Brain - Cerebellar Hemisphere  105  Brain  Brain
 Brain - Cerebellum  125  Brain  Brain
 Brain - Cortex  114  Brain  Brain
 Brain - Frontal Cortex (BA9)  108  Brain  Brain
 Brain - Hippocampus  94  Brain  Brain
 Brain - Hypothalamus  96  Brain  Brain
 Brain - Nucleus accumbens (basal ganglia)  113  Brain  Brain
 Brain - Putamen (basal ganglia)  97  Brain  Brain
 Brain - Spinal cord (cervical c-1)  71  Brain  Brain
 Brain - Substantia nigra  63  Brain  Brain
 Breast - Mammary Tissue  214  Breast  Reproductive
 Cells - EBV-transformed lymphocytes  118  Blood  Other
 Cells - Transformed fibroblasts  284  Skin  Other
 Cervix - Ectocervix  6  Cervix Uteri  Reproductive
 Cervix - Endocervix  5  Cervix Uteri  Reproductive
 Colon - Sigmoid  149  Colon  Digestive
 Colon - Transverse  196  Colon  Digestive
 Esophagus - Gastroesophageal Junction  153  Esophagus  Digestive
 Esophagus - Mucosa  286  Esophagus  Digestive
 Esophagus - Muscularis  247  Esophagus  Digestive
 Fallopian Tube  6  Fallopian Tube  Reproductive
 Heart - Atrial Appendage  194  Heart  Cardiovascular
 Heart - Left Ventricle  218  Heart  Cardiovascular
 Kidney - Cortex  32  Kidney  Other
 Liver  119  Liver  Digestive
 Lung  320  Lung  Other
 Minor Salivary Gland  57  Salivary Gland  Other
 Muscle - Skeletal  430  Muscle  Other
 Nerve - Tibial  304  Nerve  Other
 Ovary  97  Ovary  Reproductive
 Pancreas  171  Pancreas  Digestive
 Pituitary  103  Pituitary  Endocrine
 Prostate  106  Prostate  Reproductive
 Skin - Not Sun Exposed (Suprapubic)  250  Skin  Other
 Skin - Sun Exposed (Lower leg)  357  Skin  Other
 Small Intestine - Terminal Ileum  88  Small Intestine  Digestive
 Spleen  104  Spleen  Other
 Stomach  193  Stomach  Digestive
 Testis  172  Testis  Reproductive
 Thyroid  323  Thyroid  Endocrine
 Uterus  83  Uterus  Reproductive
 Vagina  96  Vagina  Reproductive
 Whole Blood  393  Blood  Other
View table schema
Data last updated: 2020-01-21

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 51 tissues and 2 cell lines, based on RNA-seq data from the GTEx midpoint milestone data release (V6, October 2015). This release is based on data from 8555 tissue samples obtained from 570 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 platform to produce 76-bp paired end reads at a depth averaging 50M aligned reads per sample. Sequence reads were aligned to the hg19/GRCh37 human genome using Tophat v1.4.1 assisted by the GENCODE v19 transcriptome definition. Gene annotations were produced by taking the union of the GENCODE exons for each gene. Gene expression levels in RPKM were called via the RNA-SeQC tool, 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 RPKM 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. 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

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.

  • 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. 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