Functional-Network-Based Gene Set Analysis Using Gene-Ontology

Billy Chang, Rafal Kustra and Weidong Tian

PLOS ONE, 2013, vol. 8, issue 2, 1-13

Abstract: To account for the functional non-equivalence among a set of genes within a biological pathway when performing gene set analysis, we introduce GOGANPA, a network-based gene set analysis method, which up-weights genes with functions relevant to the gene set of interest. The genes are weighted according to its degree within a genome-scale functional network constructed using the functional annotations available from the gene ontology database. By benchmarking GOGANPA using a well-studied P53 data set and three breast cancer data sets, we will demonstrate the power and reproducibility of our proposed method over traditional unweighted approaches and a competing network-based approach that involves a complex integrated network. GOGANPA’s sole reliance on gene ontology further allows GOGANPA to be widely applicable to the analysis of any gene-ontology-annotated genome.

Date: 2013
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0055635

DOI: 10.1371/journal.pone.0055635

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