CASSys: an integrated software-system for the interactive analysis of ChIP-seq data
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CASSys: an integrated software-system for the interactive analysis of ChIP-seq data. / Alawi, Malik; Kurtz, Stefan; Beckstette, Michael.
in: J INTEGR BIOINFORMAT, Jahrgang 8, Nr. 2, 2011, S. 155.Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung
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TY - JOUR
T1 - CASSys: an integrated software-system for the interactive analysis of ChIP-seq data
AU - Alawi, Malik
AU - Kurtz, Stefan
AU - Beckstette, Michael
PY - 2011
Y1 - 2011
N2 - The mapping of DNA-protein interactions is crucial for a full understanding of transcriptional regulation. Chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) has become the standard technique for analyzing these interactions on a genome-wide scale. We have developed a software system called CASSys (ChIP-seq data Analysis Software System) spanning all steps of ChIP-seq data analysis. It supersedes the laborious application of several single command line tools. CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection) to various follow-up analyses. The latter are accessible via a state-of-the-art web interface and can be performed interactively by the user. The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative binding motifs, the identification of over-represented Gene Ontology-terms, pathway analysis and the visualization of interaction networks. The system is client-server based, accessible via a web browser and does not require any software installation on the client side. To demonstrate CASSys's functionality we used the system for the complete data analysis of a publicly available Chip-seq study that investigated the role of the transcription factor estrogen receptor-α in breast cancer cells.
AB - The mapping of DNA-protein interactions is crucial for a full understanding of transcriptional regulation. Chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) has become the standard technique for analyzing these interactions on a genome-wide scale. We have developed a software system called CASSys (ChIP-seq data Analysis Software System) spanning all steps of ChIP-seq data analysis. It supersedes the laborious application of several single command line tools. CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection) to various follow-up analyses. The latter are accessible via a state-of-the-art web interface and can be performed interactively by the user. The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative binding motifs, the identification of over-represented Gene Ontology-terms, pathway analysis and the visualization of interaction networks. The system is client-server based, accessible via a web browser and does not require any software installation on the client side. To demonstrate CASSys's functionality we used the system for the complete data analysis of a publicly available Chip-seq study that investigated the role of the transcription factor estrogen receptor-α in breast cancer cells.
KW - Animals
KW - Binding Sites
KW - Chromatin Immunoprecipitation
KW - DNA-Binding Proteins
KW - Estrogen Receptor alpha
KW - Genomics
KW - High-Throughput Nucleotide Sequencing
KW - Humans
KW - Oligonucleotide Array Sequence Analysis
KW - Software
KW - Transcription Factors
U2 - 10.2390/biecoll-jib-2011-155
DO - 10.2390/biecoll-jib-2011-155
M3 - SCORING: Journal article
C2 - 21690655
VL - 8
SP - 155
JO - J INTEGR BIOINFORMAT
JF - J INTEGR BIOINFORMAT
SN - 1613-4516
IS - 2
ER -