Welcome to GeneFriends ---RNAseq---

GeneFriends employs a RNAseq based gene co-expression network for candidate gene prioritization, based on a seed list of genes, and for functional annotation of unknown genes in human and mouse.

For more details on how to use GeneFriends click here

Gene query

Input a gene or list of gene/transcript IDs to obtain co-expressed genes/transcripts and their respective functional enrichment.

Select ID type. If left blank GeneFriends will guess the type of ID used.

Enter one or more gene identifiers

How do I use this tool?

GeneFriends is a functional genomics tool aimed at biologists and clinicians. It is based on a gene co-expression map that describes which genes tend to be activated (increase in expression) and deactivated (decrease in expression) simultaneously in a large number of RNAseq data samples. Because the samples originate from a wide range of conditions, the co-expression map reflects which genes in general tend to be activated simultaneously and are thus under similar transcriptional regulation. This information can be used statistically, using a guilt-by-association approach, to identify and prioritize novel candidate genes involved in biological processes and complex diseases for which a seed list of genes associated with that disease or process is available. It can also be used to gain insights on genes of unknown function by looking at which genes they are co-expressed with. A detailed description of the RNAseq based version of GeneFriends is available in our about section and our latest publication.

We constructed a co-expression map for human (46475 samples) and mouse (34322 Samples).

NOTE: The database behind the RNAseq based map is larger than 1 TB, for which reason some features may take up to a minute to load. We kindly ask you to be patient and not resubmit queries whilst the web page is loading.

Overall, GeneFriends can be used to:

  1. Assign putative functions to poorly annotated genes/features.
  2. Identify and rank new candidate genes/features related to a disease or biological process from a seed list of genes/features.

The microarray based version of this tool is also available.

A brief tutorial on how to use GeneFriends: