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Using CisGenome to Analyze ChIP-chip and ChIP-seq Data.
Curr Protoc Bioinformatics. 2011 Mar;Chapter 2:Unit2.13
Authors: Ji H, Jiang H, Ma W, Wong WH
Chromatin immunoprecipitation (ChIP) coupled with genome tiling array hybridization (ChIP-chip) and ChIP followed by massively parallel sequencing (ChIP-seq) are high-throughput 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.Curr. Protoc. Bioinform. 33:2.13.1-2.13.45. © 2011 by John Wiley & Sons, Inc.
PMID: 21400695 [PubMed - in process]
More...
Using CisGenome to Analyze ChIP-chip and ChIP-seq Data.
Curr Protoc Bioinformatics. 2011 Mar;Chapter 2:Unit2.13
Authors: Ji H, Jiang H, Ma W, Wong WH
Chromatin immunoprecipitation (ChIP) coupled with genome tiling array hybridization (ChIP-chip) and ChIP followed by massively parallel sequencing (ChIP-seq) are high-throughput 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.Curr. Protoc. Bioinform. 33:2.13.1-2.13.45. © 2011 by John Wiley & Sons, Inc.
PMID: 21400695 [PubMed - in process]
More...