How To Interpret The Results Of De Novo Motif Discovery?

Question

[Gahoo]

As we know, we can obtain the sequence motif from promoter sequences of differentially expressed genes derived from microarray experiments by de novo motif discovery tools such as MEME, GimmeMotifs. The question is how to interpret the motifs besides saying that they might be related to a certain biological process? What could we do except for drawing sequence logo and comparing to the known motifs in TRANSFAC or JASPAR? What could we do to further interpret the results?

Answer 1

[Larry_Parnell]

For one, if you feel that the motif is indicative of regulation of genes in response to factor X or condition Y, then see if there is an enrichment of genes carrying that motif when factor X or condition Y is applied to the cells/tissue/organism. In short, the motif is generally proposed to regulate gene expression, so use gene expression data to confirm or deny that function of the motif.

[Gahoo]

Thanks for your answer. But how to identify such enrichment? Would Gene Ontology be helpful?