The objective of this chapter is to describe step-by-step bioinformatics and functional genomics solutions for analyzing ChIP-Seq and RNA-Seq data for understanding the regulatory mechanisms of chromatin modifiers and transcription factors that can drive pathogenesis of chronic complex human diseases, such as cancer. Here we have used two transcription regulatory proteins: nuclear respiratory factor 1 (NRF1) and inhibitor of differentiation protein 3 (ID3) for ChIP-Seq and RNA-Seq data as examples for discussing the importance of selecting the appropriate computational analysis methods, software, and parameters for the processing of raw data as well as their integrative regulatory landscape analysis to obtain accurate and reliable results. Both ChIP-Seq and RNA-Seq analytic methodologies are used as instructional examples to identify NRF1 or ID3 binding to the promoters and enhancers in the genome and their effects on the activity as well as to discover target genes that can drive breast cancer.
Keywords: Bioinformatics; ID3; Integrated ChIP-Seq and RNA-Seq; NRF1; Transcription factor.