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

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 researchers at the University of Liverpool 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, this updated tool allows candidate transcripts to be linked to diseases and processes using a guilt-by-association approach.


A graphical overview of the steps involved in retrieving results from GeneFriends

Availability – GeneFriends is freely available from

van Dam S, Craig T, de Magalhães JP. (2014) GeneFriends: a human RNA-seq-based gene and transcript co-expression database. Nucleic Acids Res [Epub ahead of print]. [article]

The microarray based version of this tool is also available.

A brief tutorial on how to use GeneFriends:

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