Gene query

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

Human (Homo sapiens) Mouse (Mus musculus)

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

ArrayExpress gene ID Ensembl gene ID Entrez gene ID GenomeRNAi ID Gene Symbol HGNC gene ID MIM gene ID miRBase ID RefSeq Gene ID RefSeq Protein ID TransFac ID UCSC gene ID Unigene ID UniProt ID VEGA gene ID Ensembl Transcript ID HAVANA Transcript ID HGNC Transcript ID miRBaseTranscript ID Rfam Transcript ID Uniprot Transcript ID VEGA Transcript ID

Enter one or more gene identifiers

Show example 1 Show example 2
List of gene identifiers: Search

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). In addition to this we also constructed co-expression maps for TCGA (11284 samples) and GTEx (9662 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: