A comprehensive analysis workflow for genome-wide screening data from ChIP-sequencing experiments

Hatice Gulcin Ozer, Doruk Bozdaǧ, Terry Camerlengo, Jiejun Wu, Yi Wen Huang, Tim Hartley, Jeffrey D. Parvin, Tim Huang, Umit V. Catalyurek, Kun Huang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

ChIP-sequencing is a new technique for generating short DNA sequences useful in analyzing DNA-protein interactions and carrying out genome- wide studies. Although there are some studies to process and analyze ChIP-sequencing data, a complete workflow has not been reported yet. The size of the data and broad range of biological questions are the main challenges to establish a data analysis workflow for ChIP-sequencing data. In this paper, we present the ChIP-sequencing data analysis workflow that we developed at the Ohio State University Comprehensive Cancer Center Bioinformatics Shared Resources. This pipeline utilizes 1) use of different mapping algorithms such as Eland, MapReads, SeqMap, RMAP to align short sequence reads to the reference genome 2) a novel normalization algorithm to detect significant binding densities and to compare binding densities of different experiments 3) gene database mapping and 3D binding density visualization 4) distributed computing and high performance computing (HPC) supprt.

Original languageEnglish (US)
Title of host publicationBioinformatics and Computational Biology - First International Conference, BICoB 2009, Proceedings
Pages320-330
Number of pages11
DOIs
StatePublished - Aug 11 2009
Externally publishedYes
Event1st International Conference on Bioinformatics and Computational Biology, BICoB 2009 - New Orleans, LA, United States
Duration: Apr 8 2009Apr 10 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5462 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other1st International Conference on Bioinformatics and Computational Biology, BICoB 2009
CountryUnited States
CityNew Orleans, LA
Period4/8/094/10/09

Keywords

  • ChIP-seq
  • Normalization
  • Parallelization
  • Short sequence mapping
  • Visualization
  • Workflow

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Ozer, H. G., Bozdaǧ, D., Camerlengo, T., Wu, J., Huang, Y. W., Hartley, T., Parvin, J. D., Huang, T., Catalyurek, U. V., & Huang, K. (2009). A comprehensive analysis workflow for genome-wide screening data from ChIP-sequencing experiments. In Bioinformatics and Computational Biology - First International Conference, BICoB 2009, Proceedings (pp. 320-330). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5462 LNBI). https://doi.org/10.1007/978-3-642-00727-9_30