Which gene set libraries are available for pathway BMD analysis?

FastBMD supports enrichment analysis with gene sets from the Gene Ontology, PANTHER, KEGG, Reactome, and MSigDB databases. Note - not all gene set libraries are available for all species.

The GO:BP, GO:MF, and GO:CC gene sets include the complete set of Gene Ontology terms (> 45 000) for the biological process, molecular function, and cellular component categories.

The PANTHER:BP, PANTHER:MF, and PANTHER:CC are reduced sets of GO terms (“GO slims”) that have been manually chosen based on the PANTHER protein classification system. Briefly, the PANTHER project has created > 15 000 phylogenetic trees that encode the evolutionary relationships within protein families. Subsets of GO terms were chosen that best reflect the function gain or loss along the branches of the PANTHER trees for each of the BP, MF, and CC categories. In general, GO slims can simplify the interpretation of enrichment analysis results because they reduce the number of highly similar GO terms.

The KEGG and Reactome gene sets represent biological pathways and processes. KEGG pathways are also based on molecular interactions in the primary literature, but are accompanied by an extensive ortholog mapping that allows KEGG pathways to be rapidly extended to additional species based on genome sequence homology. Reactome pathways are created through a process similar to scientific peer review, where different experts create and review the pathway organization, and all interactions contain references to the primary literature.