The input to the motif analysis is a set of peaks. When you're doing the motif analysis, you're trying to find if there's particular motif enriched in your set of peaks. And these motifs can be things like transcription factors or zinc finger binding proteins.

This is useful because it provides you with a sort of validation of your data.

  1. For example, if you know the protein that you're targeting is associated with  a particular transcription factor, when you do the motif analysis, that transcription factor should hopefully show up as enriched in your peaks. 
  2. Another way it can be useful is say if you're comparing a treatment versus control, and maybe you get the set of peaks that change between the treatment versus control. With the motif analysis you might find that there's an enrichment for a particular transcription factor. This may mean that the transcription factor changes in expression between the treatment and control.

Like pathway analysis, motif analysis gives you a more granular view of the biology in your ChIP-seq samples and what's going on. After all, when you're looking at hundreds or thousands of peaks, that's a lot of data! But with motif analysis, you can see a more granular view, like what biology is related to these peaks. And that can be useful when you're comparing various groups of samples.