Promoter features related to tissue specificity as measured by Shannon entropy

Table 6 Over-represented Gene Ontology (GO) terms for cellular component and biological process of genes by promoter class

	Cellular component/biological process	Human only	Mouse only
CGI-/TATA+	Extracellular, extracellular space	-	Intermediate filament (cytoskeleton)
	Response to stimulus	Cell-cell signaling, organismal physiological process, inflammatory response, innate immune response, response to pest/pathogen/parasite	-
CGI+/TATA-	Cell, cytoplasm, intracellular, mitochondrion	Nucleus, ribonucleoprotein complex	-
	-	Nucleobase, nucleoside, nucleotide and nucleic acid metabolism, intracellular transport, metabolism, protein transport, intracellular protein transport, RNA processing, RNA metabolism, cell cycle, mitotic cell cycle	-
CGI-/TATA-	(Integral to) (plasma) membrane	-	Extracellular, extracellular space
	Organismal physiological process, defense response, immune response, response to biotic stimulus, response to stimulus, response to external stimulus	Response to pest/pathogen/parasite, cell communication, response to wounding, cellular defense response, signal transduction	Complement activation, complement activation (classical pathway), humoral defense mechanism (sensu Vertebrata), humoral immune response

All terms were selected using a p-value ≤ 0.05 (corrected for multiple testing). Terms common to human and mouse are listed in the second column. The two columns on the right indicate any additional terms found in only one species. The CGI-/TATA+ terms are consistent with a model of strong condition-specific induction, CGI+/TATA- terms are consistent with housekeeping functions. CGI-/TATA- terms indicate support for cell sensing and communication functions. No significant results were found for CGI+/TATA+ genes.

ISSN: 1474-760X