Using the bioconductor geneanswers package to interpret gene lists

Gang Feng, Pamela Shaw, Steven T. Rosen, Simon M. Lin*, Warren A. Kibbe

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

22 Scopus citations

Abstract

Use of microarray data to generate expression profiles of genes associated with disease can aid in identification of markers of disease and potential therapeutic targets. Pathway analysis methods further extend expression profiling by creating inferred networks that provide an interpretable structure of the gene list and visualize gene interactions. This chapter describes GeneAnswers, a novel gene-concept network analysis tool available as an open source Bioconductor package. GeneAnswers creates a gene-concept network and also can be used to build protein-protein interaction networks. The package includes an example multiple myeloma cell line dataset and tutorial. Several network analysis methods are included in GeneAnswers, and the tutorial highlights the conditions under which each type of analysis is most beneficial and provides sample code.

Original languageEnglish (US)
Title of host publicationNext Generation Microarray Bioinformatics
Subtitle of host publicationMethods and Protocols
EditorsJunbai Wang, Tianhai Tian, Aik Choon Tan
Pages101-112
Number of pages12
DOIs
StatePublished - Jan 2 2012

Publication series

NameMethods in Molecular Biology
Volume802
ISSN (Print)1064-3745

Keywords

  • Bioconductor
  • Disease ontology
  • Gene ontology
  • GeneAnswers
  • Network
  • Pathway analysis

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Feng, G., Shaw, P., Rosen, S. T., Lin, S. M., & Kibbe, W. A. (2012). Using the bioconductor geneanswers package to interpret gene lists. In J. Wang, T. Tian, & A. C. Tan (Eds.), Next Generation Microarray Bioinformatics: Methods and Protocols (pp. 101-112). (Methods in Molecular Biology; Vol. 802). https://doi.org/10.1007/978-1-61779-400-1_7