Gene-Association Files

A gene-association file links genes in a genome with one or more attributes. For example, a gene can be associated with a molecular function, chromosome location, or biological pathway.

Pre-packaged Files

GeneMerge is packaged with Gene Ontology (GO) species annotations including both specific and higher-order (all parent term) files for all three GO namespaces (molecular function, biological process, and cellular component) as well as other types of gene-association files for select species such as chromosome location. You can also download these files individually or as a package.

Custom Files

While GO analysis is common, testing for the statistical enrichment of other gene associations can provide complementary or novel biological insight. Examples of such associations include expression localization, spatial proximity in the nucleus, literature references, or even a gene's status in another genomic experiment. Many types of gene-association tests are in fact possible.

To facilitate such analyses, GeneMerge uses a generic, easy-to-construct file format to represent gene-association data which allows you to test any discrete, gene or locus-based attribute for statistical over-representation in any genome.

You need only create two text files with the following formats:

Gene Association file
genename tab ID;
genename tab ID;
genename tab ID;ID;ID;

Description file
ID tab description of function
ID tab description of function
ID tab description of function

Here, ' tab ' denotes the tab character. Note that more than one ID can be associated with each gene by separating IDs using a semi-colon.

For more information on how to create your own gene-association files please see the GeneMerge Manual.