GOMO -- Gene Ontology for MOtifs
The purpose of GOMO is to identify possible roles (Gene Ontology terms) for DNA binding motifs.
GOMO returns a list of GO-terms that are significantly associated with target genes of the motif, sorted by E-value.
Gene Ontology provides a controlled vocabulary to describe gene and gene product attributes in any organism.
GOMO takes a motif and scores each upstream region from the selected organism according to its binding affinity for the motif. Using these scores and a mapping of the upstream regions to the GO terms for the organism, GOMO determines which GO terms are associated with the (putative) target genes of the binding motif. GOMO reports E-values for each GO-term as well as q-values determined by the method of Benjamini and Hochberg (where q-value is defined as the minimal false discovery rate at which a given GO-term occurrence is deemed significant). GOMO reports all GO terms with E-values smaller than a specified threshold.
To score upstream regions, the GOMO web service can use either the average binding affinity score, which computes the average likelihood ratio of all positions in a sequence, or the maximum binding affinity score, which computes the maximum likelihood ratio score of all positions in the sequence. Both of these scores are computed using the AMA MEME Suite tool.