Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset

作者: Lihua Julie Zhu

DOI: 10.1007/978-1-62703-607-8_8

关键词: DNA binding siteIn vivoProtein dnaTranscription factorBinding siteGene expressionGene regulatory networkEpigeneticsChromatin immunoprecipitationHistoneComputer scienceComputational biology

摘要: Epigenetic regulation and interactions between transcription factors regulatory genomic regions play crucial roles in controlling transcriptional networks that drive development, environmental responses, disease. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) ChIP tiling microarray hybridization (ChIP-chip) are the two of most widely used technologies for genome-wide identification DNA protein histone modification vivo. Many algorithms tools have been developed evaluated allow factor binding sites from ChIP-seq or ChIP-chip datasets. However, site is only first step; ultimate goal to discover network (TF). Here, we present a common workflow downstream analysis with an emphasis on annotating integration gene expression data identify direct indirect targets TF. These will help overall unraveling using datasets publicly available GEO.

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