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Hello all,
I was wondering what is the right approach to the problem of finding relative enrichment of two motifs for two different transcription factors? People frequently look for cofactors in this way; however I was not sure if there is a specific way to do it systematically? Mostly you just see people run MEME on sequences that they get from ChIP-seq and look for off-center motifs. Is there a better way to find hypothetical co-factors?
I was wondering what is the right approach to the problem of finding relative enrichment of two motifs for two different transcription factors? People frequently look for cofactors in this way; however I was not sure if there is a specific way to do it systematically? Mostly you just see people run MEME on sequences that they get from ChIP-seq and look for off-center motifs. Is there a better way to find hypothetical co-factors?