Welcome to GeneFriends


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

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 microarray datasets. Because the microarray datasets come 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 GeneFriends has been published.

We constructed co-expression maps for humans and for various model organisms (mice, rats, flies and yeast). Because more data is available for humans and mice, however, GeneFriends is expected to be more accurate for these two species.

NOTE: The GeneFriends website has been updated (22-01-2014). This mostly entails a number of changes to increase the speed at which the website retrieves results, which them self remain unchanged. Additionally small changes have been made to the downloadable results. One of the primary changes is that the output now include all co-expressed genes rather than only the 5 percentile.

Overall, GeneFriends can be used to:

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

Search

Gene query

Input a gene or list of genes to obtain co-expressed genes (and identify new candidate genes possibly associated with the query genes) and their respective functional enrichment.

Select ID type. If left blank GeneFriends will guess the type of ID used (Usually this will work, but some IDs are not unique to one type. If this is the case GeneFriends may select the wrong identifier type)

Enter one or more gene IDs.