Table 1. A summary of ontologies, infrastructures and functions included in dcGOR.

	Description
Ontologies
Gene Ontology	Knowledge on functions; annotate domains from SCOP, Pfam, InterPro and RNA families from Rfam
Disease Ontology	Knowledge on human diseases; annotate SCOP domains only
Human Phenotype	Knowledge on human phenotypes; annotate SCOP domains only
Mammalian Phenotype	Knowledge on mouse phenotypes; annotate SCOP domains only
Enzyme Commission	Knowledge on enzyme activities; annotate SCOP domains only
UniProtKB KeyWords	Knowledge on functions and others; annotate SCOP domains only
UniProtKB UniPathway	Knowledge on pathways; annotate SCOP domains only
Infrastructures
InfoDataFrame	S4 class for representing data information (e.g. domains)
Onto	S4 class for representing ontologies
Anno	S4 class for representing domain-centric annotations
Eoutput	S4 class for storing enrichment outputs
Dnetwork	S4 class for storing domain networks
Coutput	S4 class for storing RWR-based contact outputs
Cnetwork	S4 class for storing contact networks
Functions for customised data building
dcBuildInfoDataFrame	Create an object of S4 class ‘InfoDataframe’ from an input file
dcBuildOnto	Create an object of S4 class ‘Onto’ from input files
dcBuildAnno	Create an object of S4 class ‘Anno’ from input files
Functions for analysis and visualisation
dcEnrichment	Enrichment analysis; return an object of S4 class ‘Eoutput’
visEnrichment	Enrichment output visualisation
dcDAGdomainSim	Semantic similarity calculation; return an object of S4 class ‘Dnetwork’
dcRWRpipeline	Random walk with restart; return an object of S4 class ‘Coutput’
dcDAGannotate	Annotation propagation according to true-path rule
dcConverter	Conversion between different graph classes
dcRDataLoader	Loading RData into the current environment