xIP-seq platform: An integrative framework for high-throughput sequencing data analysis

Xin Wang, Mingxiang Teng, Guohua Wang, Yuming Zhao, Xu Han, Weixing Feng, Lang Li, Jeremy Sanford, Yunlong Liu

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

2 Scopus citations

Abstract

We report an integrative bioinformatic platform for next-generation sequencing data analysis, xIP-seq, which is built on GenePattern package. The purpose for this tool is to provide analysis pipelines for data derived from next-generation sequencing following a variety of experiments using immunoprecipitation, such as ChIP-seq (chromatin immunoprecipitation following sequencing) for analysis of DNA binding protein, CLIP-seq (cross-linking immunoprecipitation following sequencing) for analysis of RNA binding protein, and MeDIP-seq (methylation DNA immunoprecipitation following sequencing) for DNA methylation profiles. xIP-seq platform provides standardized data pre-processing workflows which prepare raw data from various sequencing platforms for further analysis, and several bioinformatic applications including sequence annotation and analysis of Pol II binding pattern and histone modification.. The tertiary module for sequence annotation is particularly discussed. xIP-seq also allows users to construct new analysis pipelines tailored for individual biological interests by employing currently available modules or creating new ones. As an example, a "CLIP-seq Mapper" pipeline is created to map CLIP-seq-derived data to human genome to identify the genome-wide annotation of SFRS1 binding pattern. This implementation demonstrates the significance of xIP-seq platform to analyze massive amounts of next-generation sequencing data and provide automatic, flexible, and intelligent enterprise-level bioinformatic solutions. Availability: http://watson.compbio. iupui.edu:8081/gp.

Original languageEnglish (US)
Title of host publicationOCCBIO'09
Subtitle of host publication2009 Ohio Collaborative Conference on Bioinformatics
Pages26-31
Number of pages6
DOIs
StatePublished - Nov 2 2009
Event2009 Ohio Collaborative Conference on Bioinformatics, OCCBIO 2009 - Cleveland, OH, United States
Duration: Jun 15 2009Jun 17 2009

Publication series

NameOCCBIO'09: 2009 Ohio Collaborative Conference on Bioinformatics

Other

Other2009 Ohio Collaborative Conference on Bioinformatics, OCCBIO 2009
CountryUnited States
CityCleveland, OH
Period6/15/096/17/09

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Keywords

  • Bioinformatics
  • GenePattern
  • Module
  • Next generation sequencing
  • Pipeline
  • Sequencing

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Wang, X., Teng, M., Wang, G., Zhao, Y., Han, X., Feng, W., Li, L., Sanford, J., & Liu, Y. (2009). xIP-seq platform: An integrative framework for high-throughput sequencing data analysis. In OCCBIO'09: 2009 Ohio Collaborative Conference on Bioinformatics (pp. 26-31). [5159156] (OCCBIO'09: 2009 Ohio Collaborative Conference on Bioinformatics). https://doi.org/10.1109/OCCBIO.2009.20