How to query our gene2pheno database directly
We have opened direct access to the gene2pheno database, where we are hosting the PrediXcan results of close to 3000 phenotypes (from public GWAS meta analysis results and UKBiobank results from Ben Neale/HAIL team).
Below are R functions that will allow you access and query the database. These results are based on GTEx V6p models and details of the analysis can be found in our preprint link to preprint in press now in Nature Communications.
Usual disclaimers apply. This is provided for your convenience and with the hope of being useful. We provide no guarantee of accuracy etc…
| ### Via PostgreSQL |
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| ### Via BigQuery If you have a Google Cloud Platform account (you can get a free account with a small credit included in Google Cloud) you can query directly from the webpages |
| - PrediXcan Association UKBiobank - Predictdb prediction models - Heritability Estimates from this paper |
Via gene2pheno.org
Of course you can also query using our app link
| If you find our resources useful please cite our papers so that we can continue maintaining them. |
| ## Reference - Gamazon ER†, Wheeler HE†, Shah KP†, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC, Nicolae DL, Cox NJ, Im HK. (2015) A gene-based association method for mapping traits using reference transcriptome data. Nat Genet. doi:10.1038/ng.3367. (Link to paper, Link to Preprint on BioRxiv) |
| - Alvaro N. Barbeira, Scott P. Dickinson, Jason M. Torres, Rodrigo Bonazzola, Jiamao Zheng, Eric S. Torstenson, Heather E. Wheeler, Kaanan P. Shah, Todd Edwards, Tzintzuni Garcia, GTEx Consortium, Dan Nicolae, Nancy J. Cox, Hae Kyung Im (2017) Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics link to preprint In press in Nature Communications 2018 |
| - Heather E Wheeler, Kaanan P Shah, Jonathon Brenner, Tzintzuni Garcia, Keston Aquino-Michaels, GTEx Consortium, Nancy J Cox, Dan L Nicolae, Hae Kyung Im. (2016) Survey of the Heritability and Sparsity of Gene Expression Traits Across Human Tissues. link to paper |
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