Gene Ontology, Enrichment Analysis, and Pathway Analysis

With various sequence datasets including peptide sequences, genes, expressed sequence tags (ESTs), microarray datasets, RNA-Seq datasets, or whole genome sequences, gene ontology (GO) analysis provides defined GO terms to genes. At the highest level, GO terms cover cellular components, molecular functions, and biological processes. Lower levels of GO terms can be applied to genes when relevant. GO database is very suitable for enrichment analysis on gene sets. GO has become one of the most popular annotation sources. The functional annotation tool mainly provides batch annotation and enrichment analysis. The functional annotation tool can display genes from a user's list on pathway maps to facilitate biological interpretation in a network context. This chapter introduces some of the major pathway databases. It then discusses the three generations of knowledge-driven pathway analysis that may be useful for users to select proper pathway analysis tools, such as Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Mapping.