gnomAD gnomAD pext Track Settings
 
gnomAD Proportion Expression Across Transcript Scores (pext)

Track collection: Genome Aggregation Database (gnomAD) - Variants, Coverage, and Constraint

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 Mean Proportion  gnomAD pext Mean Proportion   Schema 
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 Adipose-Subcut  gnomAD pext Adipose-Subcutaneous   Schema 
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 Adipose-Visceral (Omentum)  gnomAD pext Adipose-Visceral (Omentum)   Schema 
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 Adrenal Gland  gnomAD pext Adrenal Gland   Schema 
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 Artery-Aorta  gnomAD pext Artery-Aorta   Schema 
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 Artery-Coronary  gnomAD pext Artery-Coronary   Schema 
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 Artery-Tibial  gnomAD pext Artery-Tibial   Schema 
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 Bladder  gnomAD pext Bladder   Schema 
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 Brain-Amygdala  gnomAD pext Brain-Amygdala   Schema 
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 Brain-Anterior Cingulate Cortex (BA24)  gnomAD pext Brain-Anterior Cingulate Cortex (BA24)   Schema 
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 Brain-Caudate (basal ganglia)  gnomAD pext Brain-Caudate (basal ganglia)   Schema 
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 Brain-Cerebellar Hemisphere  gnomAD pext Brain-Cerebellar Hemisphere   Schema 
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 Brain-Cerebellum  gnomAD pext Brain-Cerebellum   Schema 
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 Brain-Cortex  gnomAD pext Brain-Cortex   Schema 
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 Brain-Frontal Cortex (BA9)  gnomAD pext Brain-Frontal Cortex (BA9)   Schema 
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 Brain-Hippocampus  gnomAD pext Brain-Hippocampus   Schema 
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 Brain-Hypothalamus  gnomAD pext Brain-Hypothalamus   Schema 
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 Brain-Nucleus Accumbens (basal ganglia)  gnomAD pext Brain-Nucleus Accumbens (basal ganglia)   Schema 
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 Brain-Putamen (basal ganglia)  gnomAD pext Brain-Putamen (basal ganglia)   Schema 
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 Brain-Spinal Cord (cervicalc 1)  gnomAD pext Brain-Spinal Cord (cervicalc 1)   Schema 
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 Brain-Substantia Nigra  gnomAD pext Brain-Substantia Nigra   Schema 
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 Breast-Mammary Tissue  gnomAD pext Breast-Mammary Tissue   Schema 
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 Cells-EBV-transformed Lymphocytes  gnomAD pext Cells-EBV-transformed Lymphocytes   Schema 
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 Cells-Transformed Fibroblasts  gnomAD pext Cells-Transformed Fibroblasts   Schema 
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 Cervix-Ectocervix  gnomAD pext Cervix-Ectocervix   Schema 
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 Cervix-Endocervix  gnomAD pext Cervix-Endocervix   Schema 
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 Colon-Sigmoid  gnomAD pext Colon-Sigmoid   Schema 
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 Colon-Transverse  gnomAD pext Colon-Transverse   Schema 
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 Esophagus-Gastroesophageal Junction  gnomAD pext Esophagus-Gastroesophageal Junction   Schema 
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 Esophagus-Mucosa  gnomAD pext Esophagus-Mucosa   Schema 
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 Esophagus-Muscularis  gnomAD pext Esophagus-Muscularis   Schema 
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 Fallopian Tube  gnomAD pext Fallopian Tube   Schema 
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 Heart-Atrial Appendage  gnomAD pext Heart-Atrial Appendage   Schema 
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 Heart-Left Ventricle  gnomAD pext Heart-Left Ventricle   Schema 
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 Kidney-Cortex  gnomAD pext Kidney-Cortex   Schema 
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 Liver  gnomAD pext Liver   Schema 
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 Lung  gnomAD pext Lung   Schema 
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 Minor Salivary Gland  gnomAD pext Minor Salivary Gland   Schema 
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 Muscle-Skeletal  gnomAD pext Muscle-Skeletal   Schema 
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 Nerve-Tibial  gnomAD pext Nerve-Tibial   Schema 
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 Ovary  gnomAD pext Ovary   Schema 
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 Pancreas  gnomAD pext Pancreas   Schema 
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 Pituitary  gnomAD pext Pituitary   Schema 
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 Prostate  gnomAD pext Prostate   Schema 
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 Skin-Not Sun Exposed (Suprapubic)  gnomAD pext Skin-Not Sun Exposed (Suprapubic)   Schema 
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 Skin-Sun Exposed (Lowerleg)  gnomAD pext Skin-Sun Exposed (Lowerleg)   Schema 
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 Small Intestine-Terminal Ileum  gnomAD pext Small Intestine-Terminal Ileum   Schema 
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 Spleen  gnomAD pext Spleen   Schema 
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 Stomach  gnomAD pext Stomach   Schema 
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 Testis  gnomAD pext Testis   Schema 
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 Thyroid  gnomAD pext Thyroid   Schema 
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 Uterus  gnomAD pext Uterus   Schema 
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 Vagina  gnomAD pext Vagina   Schema 
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 Whole Blood  gnomAD pext Whole Blood   Schema 
    

Description

The gnomAD Proportion Expression Across Transcript Scores (pext) (pext) track set displays isoform expression levels across 53 tissues, based on 11,706 tissue samples from the Genotype Tissue Expression (GTEx) v7 dataset.

The gnomAD pext tracks provide a comprehensive view of the expression of exons across a gene using the proportion expression across transcripts, or pext metric, a transcript-level annotation metric that quantifies isoform expression for variants. This metric was calculated by annotating each variant with the expression of all possible consequences across all transcripts for each tissue and normalizing the expression of the annotation to the total expression of the gene, which can be interpreted as a measure of the proportion of the total transcriptional output from a gene that would be affected by the variant annotation in question.

Each of the subtracks shows the pext metric for a specific tissue, except the gnomAD pext Mean Proportion subtrack that shows the average pext metrics calculated from the 53 GTEx tissues.

Display Conventions and Configuration

The pext graphs display the mean expression at each base position for protein-coding (CDS) regions. While UTRs do have expression in transcriptome datasets, note that this information is not included for the visualization. The details page shows calculated sample percentages for the range of sequence within the browser window.

Methods

The pext values are derived from isoform quantifications using the RSEM tool. Detailed information about development and commands to create these files can be found here. Pext values were downloaded from the gnomAD website and transformed into bigWigs, one per tissue. For the full list of UCSC specific steps, please see the "gnomAD PEXT scores" section of the hg19 makedoc from our GitHub repository.

Note that isoform quantification tools can be imprecise, especially for longer genes with many annotated isoforms. Regions with low pext values might be enriched for annotation errors (ie. there may be edge cases for which an exon that is established to be critical for gene function may appear unexpressed with pext). Also note that the GTEx dataset is postmortem adult tissue, and thus the possibility that an exon may be development-specific or may be expressed in tissues not represented in GTEx can not be dismissed.

Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. The data can also be found directly from the gnomAD downloads page.

Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information.

More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site.

Credits

Thanks to the Genome Aggregation Database Consortium for making these data available, Nick Watts for developing this track on the gnomAD Browser, and Anna Benet-Pagès and Chris Lee for building this track on the UCSC Genome Browser. The data are released under the ODC Open Database License (OBdL) as described here.

References

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197

Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194

Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198