title: Using the bioconductor GeneAnswers package to interpret gene lists.
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.
authors: Biomedical Informatics Center, Clinical and Translational Sciences Institute, Northwestern University, Chicago, IL, USA.
authors: Gang
authors: G
authors: Feng
authors: Pamela
authors: P
authors: Shaw
authors: Steven T
authors: ST
authors: Rosen
authors: Simon M
authors: SM
authors: Lin
authors: Warren A
authors: WA
authors: Kibbe
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D009101:Multiple Myeloma / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software