PrediXcan

PrediXcan is a gene-based association test that prioritizes genes that are likely to be causal for the phenotype.

PredictDB

PredictDB hosts genetic prediction models of transcriptome levels to be used with PrediXcan.

The following models are available for download.

DGN Whole Blood Elastic Net SQTLite db link (A ~28MB file will be downloaded)
DGN Whole Blood Elastic Net text link (A ~18MB file will be downloaded)
DGN Whole Blood LASSO SQTLite db link (A ~18MB file will be downloaded)

G2Pdb

G2Pdb, Gene to Phenotype database, hosts the results of PrediXcan applied to a variety of phenotypes. Link to prototype. Currently, the prototype hosts the results of PrediXcan applied to WTCCC (Wellcome Trust Case Control Consoritium) diseases using DGN whole blood prediction models.

##Reference Eric R. Gamazon†, Heather E. Wheeler†, Kaanan P. Shah†, Sahar Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, GTEx Consortium, Dan L. Nicolae, Nancy J. Cox, and Hae Kyung Im* PrediXcan: Trait Mapping Using Human Transcriptome Regulation (2015 Accepted in Nature Genetics) Preprint on BioRxiv

†:equal contribution *:correspondence

##Software

Python version

Gene expression prediction script link

Perl version

Download scripts here
Download prediction model in text format here (A ~18MB file will be downloaded)

R version

Gene expression prediction script link

##Acknowledgements

DGN RNA-seq data

Data downloaded from NIMH Repository and Genomics Resource

Battle, A., Mostafavi, S., Zhu, X., Potash, J.B., Weissman, M.M., McCormick, C., Haudenschild, C.D., Beckman, K.B., Shi, J., Mei, R., et al. (2014). Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Research 24, 14–24.