Coexpression networks of 31 GTEx and 256 SRA RNA-Seq datasets

This data repository contains coexpression networks from publicly-available RNA-Seq datasets (obtained from the recount2 database) that were generated using the best workflows identified in the benchmarking study: Johnson KA, Krishnan A (2020) Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data. bioRxiv 10.1101/2020.09.22.308577.

GTEx coexpression networks
There are 62 coexpression networks built from 31 GTEx datasets (each dataset corresponding to one GTEx tissue) reconstructed using two different network-building workflows: i) CTF_CLR: Counts adjusted using TMM Factors followed by CLR transformation of the Pearson correlation coefficients; ii) CTF: Counts adjusted using TMM Factors (without any further transformation).

SRA coexpression networks
There are 256 coexpression networks built from 256 SRA datasets. Each dataset corresponds to a set of samples generated as part of the same transcriptome experiment from the same tissue. These networks are reconstructed using the top-performing workflow: CTF, Counts adjusted using TMM Factors.

Refer to the preprint for more details on the workflows and the steps used for obtaining the original datasets.