Abstract
Chromatin immunoprecipitation (ChIP) coupled with genome tiling array hybridization (ChIP-chip) and ChIP followed by massively parallel sequencing (ChIP-seq) are highthroughput approaches to profiling genome-wide protein-DNA interactions. Both technologies are increasingly used to study transcription-factor binding sites and chromatin modifications. CisGenome is an integrated software system for analyzing ChIP-chip and ChIP-seq data. This unit describes basic functions of CisGenome and how to use them to find genomic regions with protein-DNA interactions, visualize binding signals, associate binding regions with nearby genes, search for novel transcription-factor binding motifs, and map existing DNA sequence motifs to user-supplied genomic regions to define their exact locations.
Original language | English (US) |
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Pages (from-to) | 1-45 |
Number of pages | 45 |
Journal | Current Protocols in Bioinformatics |
Issue number | SUPP.33 |
DOIs | |
State | Published - Mar 2011 |
Keywords
- Chromatin immunoprecipitation
- Gene regulation
- Motif
- Next generation sequencing
- Tiling array
- Transcription factor
ASJC Scopus subject areas
- Structural Biology
- Biochemistry