RNA-Seq and ChIP-Seq studies individually provide useful information on gene expression profiles and elucidating the genomic regions and target genes that bind one or more regulatory proteins, respectively. When viewed together, the integrated analysis of the two data types within a given experimental study can identify co-regulated genes that share a gene regulatory “framework”. This type of systems biology approach can yield useful information when elucidating the global mechanisms of disease pathology and developing therapies for treating human genetic disease.
This course is broken down into a morning session, followed by an opportunity for individual consults in the afternoon. NOTE: This is the second course in a two-part series and students must have attended the entire course to obtain maximum benefit from the training.
The morning session (typically 9:00 am-12:00 pm) will focus on the integration of the ChIP-Seq and RNA-Seq and will cover the topics of: identifying overlapping ChIP-Seq peaks with RNA-expression profiles; pathway analysis of correlated ChIP-Seq target genes; visualization of ChIP-Seq peaks with RNA-Seq expression profiles; transcription Factor Binding Site (TFBS) analysis of promoters from ChIP-Seq target genes; identifying conserved TFBS patterns in orthologous promoters; genome-wide analysis of promoters sharing a conserved regulatory network. The afternoon session (typically 1:30 pm-4:30 pm) will be dedicated to individual consults with NIH research investigators.