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, phenotype, or expression location.

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. GeneMerge GO files are updated each month (as available from GO) and you can download these files separately.

Custom Files

Beyond standard GO term analysis, tests for statistical enrichment of other types of gene associations can provide novel or complementary biological insight. Examples include enrichment for molecular attributes such as expression location, spatial proximity in the nucleus, chromatin state, regulatory elements (cis, intronic, UTR), evolutionary properties, or even a gene's status in another genomic experiment.

To facilitate such analyses (and GO analyses in newly-sequenced species) 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.