Using the bioconductor GeneAnswers package to interpret gene lists.

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Feng, G; Shaw, P; Rosen, ST; Lin, SM; Kibbe, WA

Published Date

  • January 2012

Published In

Volume / Issue

  • 802 /

Start / End Page

  • 101 - 112

PubMed ID

  • 22130876

Electronic International Standard Serial Number (EISSN)

  • 1940-6029

International Standard Serial Number (ISSN)

  • 1064-3745

Digital Object Identifier (DOI)

  • 10.1007/978-1-61779-400-1_7

Language

  • eng