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Protocols

GTEx specifications

Information


Unique identifier OMICS_00271
Name GTEx
Alternative name Genotype-Tissue Expression
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 7
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainers


  • person_outline Deborah Colantuoni
  • person_outline Emmanouil Dermitzakis
  • person_outline Kristin Ardlie

Additional information


http://commonfund.nih.gov/GTEx https://www.gtexportal.org/home/documentationPage

Publications for Genotype-Tissue Expression

GTEx citations

 (324)
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Elucidating the genetic architecture of reproductive ageing in the Japanese population

2018
Nat Commun
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z
call_split See protocol

[…] re supplied default parameters were used for both approaches, and East-Asian specific LD scores and LD information were used where appropriate. Tissue enrichment was performed on tissues from the V6p GTEx release. Individual locus expression and methylation data were incorporated using Summary Mendelian Randomization (SMR). We used a subset of 1344 unrelated East Asian individuals (based on princi […]

library_books

Genome wide haplotype association analysis of primary biliary cholangitis risk in Japanese

2018
Sci Rep
PMCID: 5958065
PMID: 29773854
DOI: 10.1038/s41598-018-26112-1

[…] -values obtained from 2-sided Fisher’s exact tests. To investigate enrichments in gene expressions for SNPs in replicated haplotypes among the three blood- and liver-related tissue types available in GTEx, counts of significant cis-eQTLs (SNPs within +/−1 Mb of transcription start sites, q-value < 0.05) for haplotype SNPs were compared to the aforementioned comparison SNP set using a 2-sided Fishe […]

library_books

A joint view on genetic variants for adiposity differentiates subtypes with distinct metabolic implications

2018
Nat Commun
PMCID: 5956079
PMID: 29769528
DOI: 10.1038/s41467-018-04124-9

[…] region in the DEPICT analyses (to limit the contribution of multiple signals like RSPO3, Supplementary Fig. , Supplementary Data -).Fig. 6To follow-up this finding, we used FUMA to examine data from GTEx for tissue-specific enrichments of expression effects of genes overlapping our association results (P < 10−5 for any of BMI, WHR, or WHRadjBMI, excluding metabochip data), again separating the va […]

library_books

A whole genome sequence study identifies genetic risk factors for neuromyelitis optica

2018
Nat Commun
PMCID: 5955905
PMID: 29769526
DOI: 10.1038/s41467-018-04332-3

[…] 1) The most significant genetic marker for NMO (rs28383224) was shared between NMO-IgG+ and NMO-IgG−, suggesting that at least one shared genetic determinant exists for both conditions. Data from the GTEx project (Methods) do not suggest that rs28383224 regulates C4 expression, and the mechanism of action of rs28383224 in NMO risk remains unknown. (2) C4 CNV was associated with NMO-IgG+ but not NM […]

library_books

Inhibition of glutamate oxaloacetate transaminase 1 in cancer cell lines results in altered metabolism with increased dependency of glucose

2018
BMC Cancer
PMCID: 5948873
PMID: 29751795
DOI: 10.1186/s12885-018-4443-1

[…] : the early stage NSCLC data base GEO:GSE19188 [] and the metastatic melanoma data base GEO: GDS3966 []. GEPIA is a newly established gene expression analysis web server [], which integrates TCGA and GTEx databases, totally including 9736 cancers and 8587 normal samples, and improves the efficiency in various differential analyses. With the GEPIA web tool, we investigated the GOT1 expression patte […]

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Dramatic dysbalancing of the Wnt pathway in breast cancers

2018
Sci Rep
PMCID: 5943245
PMID: 29743726
DOI: 10.1038/s41598-018-25672-6
call_split See protocol

[…] http://firebrowse.org, cohort BRCA (Broad Institute TCGA Genome Data Analysis Center (2016): Firehose 2016_01_28 run. Broad Institute of MIT and Harvard. doi:10.7908/C11G0KM9). Most recent version of GTEX RNA-seq database (v6) has been downloaded from GTEX website.The gene list for the core 101 Wnt component genes (and all their orthologs) (Supplementary Table ) has been compiled based on the data […]


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GTEx institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; [etc.]
GTEx funding source(s)
Supported by the Common Fund of the Office of the Director, U.S. National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, NIA, NIAID, and NINDS through NIH contracts HHSN261200800001E (Leidos Prime contract with NCI), 10XS170 (NDRI), 10XS171 (Roswell Park Cancer Institute), 10X172 (Science Care Inc.), 12ST1039 (IDOX), 10ST1035 (Van Andel Institute), and HHSN268201000029C (Broad Institute) and through NIH grants R01 DA006227-17 (Univ. of Miami Brain Bank), R01 MH090941 (Univ. of Geneva), R01 MH090951 and R01 MH090937 (Univ. of Chicago), R01 MH090936 (Univ. of North Carolina–Chapel Hill), R01 MH090948 (Harvard Univ.), R01 GM104371 (Massachusetts General Hospital), and R01AG046170, R01CA163772, and U01AI111598-01 (Icahn School of Medicine, Mount Sinai).

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