GeneFriends: a human RNA-seq-based gene and transcript co-expression database

Abstract

Co-expression networks have proven effective at assigning putative functions to genes based on the functional annotation of their co-expressed partners, in candidate gene prioritization studies and in improving our understanding of regulatory networks. The growing number of genome resequencing efforts and genome-wide association studies often identify loci containing novel genes and there is a need to infer their functions and interaction partners. To facilitate this we have expanded GeneFriends, an online database that allows users to identify co-expressed genes with one or more user-defined genes. This expansion entails an RNA-seq-based co-expression map that includes genes and transcripts that are not present in the microarray-based co-expression maps, including over 10,000 non-coding RNAs. The results users obtain from GeneFriends include a co-expression network as well as a summary of the functional enrichment among the co-expressed genes. Novel insights can be gathered from this database for different splice variants and ncRNAs, such as microRNAs and lincRNAs. Furthermore, our updated tool allows candidate transcripts to be linked to diseases and processes using a guilt-by-association approach. GeneFriends is freely available from http://www.GeneFriends.org and can be used to quickly identify and rank candidate targets relevant to the process or disease under study.

Figure 1.

Exponential growth curve (log scale) of RNA-seq data taken from the Short Read Archive (SRA) (25).

Figure 2.

A graphical overview of the steps involved in retrieving results from GeneFriends: (1) Insert genes (2) Validate input (3) Retrieve co-expressed genes (4) Investigate functional enrichment (5) Visualize network of co-expressed genes using Bioloayout (6) Use Biololayout to select the network of interest selecting different thresholds.