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ChIP-seq experiments are the current method of choice for surveying the targets of DNA-binding tr...
ChIP-seq experiments are the current method of choice for surveying the targets of DNA-binding transcription factors (TFs). Motif-based sequence analysis of ChIP-seq data can provide extremely valuable insights into the biological mechanisms underlying transcriptional regulation. For example, it can determine the DNA-binding affinity (motif) of the factor, distinguish regions bound directly or indirectly by the factor, and suggest the identities of TFs that regulate cooperatively. Motif analysis can also be employed in differential mode to identify explanatory differences in the motif content of genomic regions bound by the factor under different cellular contexts. I will describe several types of motif-based analysis and give concrete examples of biological insights they can yield.