Tissue-Specific Gene Regulatory Networks

We provide several different resources in support of our paper "Understanding Tissue-Specific Gene Regulation":

Networks and data supporting the paper can be downloaded from Zenodo here.

In addition, on this webpage you can download:
(1) An R-data object containing the PANDA-predicted gene regulatory networks and tissue-specific edges for 38 tissues.
(2) A table of the tissue-specific edges estimated from the PANDA-networks.
(3) The input data and code needed to reconstruct the tissue-specific PANDA networks

More information about the input data can be found here: (i) normalized GTEx RNA-seq expression, (ii) motif, and (iii) PPI data.

Sample-Specific Gene Regulatory Networks

Below we link LIONESS-predicted sample-specific networks for 38 GTEx tissues. A subset of these tissues were analyzed in "Sexual Dimorphism in Gene Expression and Regulatory Networks across Human Tissues". Each RData file contains the set of single-sample networks associated with a tissue, with one network for each of the gene expression samples collected in that tissue. Data are stored in an object "net" that includes the name of the transcription factor (TF), target gene (Gene, Ensembl IDs), and lioness edge weights for each of the single-sample networks. WARNING: these files range in size from ~2G-55G.

Tissue-Specific eQTL Networks

The tissue-specific eQTL networks analyzed in "Exploring regulation in tissues with eQTL networks" can be downloaded here or as a bundle here.