PredictDB Data Repository



Welcome

Welcome to PredictDB! The files hosted here can be used with the Im Lab's software PrediXcan and MetaXcan. Navigate below to download one or more tissue models.

Not sure where to start? If you are new to PrediXcan and MetaXcan, we recommend starting your analyses with the DGN-HapMap Whole Blood model or one of the various GTEx-HapMap tissue models. See our FAQ and README file for more info.

Announcement

January 08, 2018

We are releasing prediction models trained on GTEx Version 7 data. We have updated our processing pipeline, and restricted to individuals of European ancestry to obtain more reliable LD data. This reduces false positive associations in the Summary Version of PrediXcan. Because of this choice, the gain in sample size relative to V6p is modest (ranging from -18 to 89), with whole blood, LCLs and fibroblasts experiencing reduced sample size. We developed a new criteria to assess model performance. We have also decided to include prediction models for both pseudogenes and lincRNAs.

While preparing GTEx V7 prediction models, we identified a few issues in the way prediction performance was estimated in the previous release (2016-09-08 release). In aggregate, these caused the prediction model performance to be overestimated. Reassuringly, predicted expression levels and the downstream associations with phenotypes remain mostly unchanged, even though prediction weights vary slightly. However, some gene/tissue pairs are no longer considered reliable.

Detailed description of the pipeline update and the effect in prediction models performance and downstream S-PrediXcan association can be found here .

We would appreciate comments to our mailing list predixcanmetaxcan@googlegroups.com


Disclaimer: the models are provided "as is", with the hope that they may be of use, without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. in no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the models or the use or other dealings in the models.

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Acknowledgements

GTEx

The Genotype-Tissue Expression (GTEx; Sample size ) project was supported by the Common Fund of the Office of the Director of the National Institutes of Health. All GTEx Data was downloaded from The database of Genotypes and Phenotypes (dbGaP).

DGN

Depression Genes and Networks (DGN; 922 whole-blood samples) Data was provided by Dr. Douglas F. Levinson. We gratefully acknowledge the resources were supported by National Institutes of Health/National Institute of Mental Health grants 5RC2MH089916 (PI: Douglas F. Levinson, M.D.; Coinvestigators: Myrna M. Weissman, Ph.D., James B. Potash, M.D., MPH, Daphne Koller, Ph.D., and Alexander E. Urban, Ph.D.) and 3R01MH090941 (Co-investigator: Daphne Koller, Ph.D.).

Funding

This work is supported by R01MH107666 (H.K.I.), K12 CA139160 (H.K.I.), R01 MH101820 (GTEx), P30 DK20595, P60 DK20595 (Diabetes Research and Training Center), P50 DA037844 (Rat Genomics), and P50 MH094267 (Conte).

Mailing List

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