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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 8, Issue 2

Issues

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

Malik Alawi
  • Center for Bioinformatics, University of Hamburg, Bundesstraße 43, D-20146 Hamburg, Germany, http://www.zbh.uni-hamburg.de Germany
  • Hamburg Center for Experimental Therapy Research (HEXT), University Medical Center Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, http://www.uke.de, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Stefan Kurtz
  • Center for Bioinformatics, University of Hamburg, Bundesstraße 43, D-20146 Hamburg, http://www.zbh.uni-hamburg.de, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Michael Beckstette
  • Corresponding author
  • Center for Bioinformatics, University of Hamburg, Bundesstraße 43, D-20146 Hamburg, http://www.zbh.uni-hamburg.de, Germany
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2011-155

Summary

The mapping of DNA-protein interactions is crucial for a full understanding of transcriptional regulation. Chromatin-immunoprecipitation followed bymassively 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.

About the article

Published Online: 2016-10-18

Published in Print: 2011-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 8, Issue 2, Pages 1–13, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2011-155.

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© 2011 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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