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 annota...

Gene set enrichment analysis (GSEA) is a statistical method to determine if predefined sets of genes are differentially expressed in different phenotypes. Predefined gene sets may be genes in a known metabolic pathway, located in the same cytogenetic band, sharing the same Gene Ontology category, or any user-defined set. In microarray experiments where no single gene shows statistically signifi...