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Table 3
Function annotation for 51 homotypic TF combinations
TFs	GO biological process categories

AP3	Cell adhesion; cellular localization; cellular process; extracellular matrix organization and biogenesis; innate immune response; intracellular transport; second-messenger-mediated signaling
CAAT*	Cell cycle; cell division [36]; cell organization and biogenesis; chromosome organization and biogenesis; DNA-dependent DNA replication; nucleobase, nucleoside, nucleotide and nucleic acid metabolism; protein localization; steroid biosynthesis
CACBINDING PROTEIN	Calcium ion transport; cellular process; intracellular signaling cascade; morphogenesis; nervous system development; organ development; regulation of signal transduction
CEBPB	Cellular carbohydrate metabolism
CETSP154	Cell organization and biogenesis; cellular localization; cellular process; organelle organization and biogenesis; protein localization; ribosome biogenesis; ubiquitin cycle; vesicle-mediated transport
CETS168	Cellular physiological process
CP2	N/A
CREB	N/A
DBP	Apoptosis; cell adhesion; endocytosis; innate immune response; intracellular signaling cascade; lipid metabolism; phosphate transport; protein kinase cascade; response to endogenous stimulus; RNA processing
DEAF1	N/A
DELTAEF1	Cell adhesion
E12	N/A
E2F1*	Cell cycle [25-28]; cholesterol metabolism; nucleobase, nucleoside, nucleotide and nucleic acid metabolism; sterol metabolism
EGR*	Apoptosis; brain development; cell cycle; cell proliferation; central nervous system development; development [49]; endocytosis; enzyme linked receptor protein signaling pathway; galactose metabolism; intracellular signaling cascade; metal ion transport; nervous system development [49]; protein amino acid phosphorylation; protein kinase cascade; small GTPase mediated signal transduction; synaptic transmission; transcription [37]; ubiquitin cycle
ETF*	Cell cycle; cell proliferation; cellular lipid metabolism; central nervous system development; dephosphorylation; endocytosis; enzyme linked receptor protein signaling pathway; gluconeogenesis; heart development; hexose biosynthesis; intracellular signaling cascade; muscle development; neurite morphogenesis [38]; programmed cell death; protein kinase cascade; regulation of nucleocytoplasmic transport; response to DNA damage stimulus; small GTPase mediated signal transduction
FAC1	Cell adhesion; cell cycle; cellular lipid metabolism; endocytosis; I-kappaB kinase/NF-kappaB cascade; intracellular signaling cascade, via spliceosome; proteolysis; secretion. carbohydrate metabolism; DNA repair; nuclear import; protein kinase cascade; protein localization; response to endogenous stimulus; RNA splicing; ubiquitin cycle; vesicle-mediated transport; cytoplasm organization and biogenesis; innate immune response; endoplasmic reticulum to Golgi vesicle-mediated transport; microtubule cytoskeleton organization and biogenesis; wound healing; protein amino acid glycosylation
FOX	N/A
FREAC7	N/A
GATA1	N/A
GC*	Apoptosis [35]; cell proliferation [35]; actin cytoskeleton organization and biogenesis; cell cycle; cellular lipid metabolism; central nervous system development; endocytosis; enzyme linked receptor protein signaling pathway; endoplasmic reticulum to Golgi vesicle-mediated transport; gluconeogenesis; hexose biosynthesis; muscle development; nervous system development; Notch signaling pathway; nucleocytoplasmic transport; protein kinase cascade; small GTPase mediated signal transduction; synaptic transmission; transmembrane receptor protein tyrosine kinase signaling pathway; ubiquitin cycle; vesicle-mediated transport
HELIOSA	Cellular physiological process; development; homophilic cell adhesion; regulation of metabolism
HNF1*	Organic anion transport [39]; innate immune response
HNF3B	Lipid metabolism; DNA metabolism
IRF7*	Immune response [40]
KROX*	Actin cytoskeleton organization and biogenesis; cell cycle; enzyme linked receptor protein signaling pathway; intracellular signaling cascade; nervous system development [50]; phosphate metabolism; regulation of neurotransmitter levels; small GTPase mediated signal transduction; system development; ubiquitin cycle
LBP1*	Apoptosis [51]; cellular process; intracellular signaling cascade; protein amino acid phosphorylation; protein kinase cascade
LDSPOLYA	Development; aromatic amino acid family metabolism; intracellular signaling cascade
LEF1TDF1	N/A
LFA1	N/A
MAZ*	Apoptosis; brain development; cell adhesion; cell cycle; cell differentiation; endocytosis; enzyme linked receptor protein signaling pathway; intracellular signaling cascade; muscle development [41]; nervous system development; development [41]; protein amino acid phosphorylation; protein kinase cascade; regulation of actin filament length; small GTPase mediated signal transduction; Wnt receptor signaling
MINI19	N/A
MMEF2	N/A
MYCMAX	Cellular metabolism; macromolecule metabolism
MZF1*	Cell proliferation [52]; cell adhesion; cell cycle; cell differentiation; cell-cell signaling; enzyme linked receptor protein signaling pathway; hemopoiesis [52]; metal ion transport; nervous system development; neurotransmitter secretion; organ development; regulated secretory pathway; regulation of transcription, DNA-dependent; skeletal development; synaptic transmission; Wnt receptor signaling pathway
NFAT*	Immune response [29-31]; homophilic cell adhesion; organ development
NMYC	Cellular physiological process
NRF2*	Organelle organization and biogenesis [42]; cellular physiological process; protein transport
OCT1	Apoptosis; cell-cell adhesion; cellular physiological process; protein transport
OSF2	N/A
PAX4	Cell proliferation; enzyme linked receptor protein signaling pathway; gamma-aminobutyric acid signaling pathway; inflammatory response; programmed cell death; regulation of kinase activity
PIT1	Proteolysis
PU1	Cell adhesion; regulation of kinase activity; regulation of transferase activity
S8*	Development [46]
SP1*	Cell differentiation [53]; cell proliferation [53]; apoptosis [35]; cell adhesion; cell cycle; cell-cell signaling; cellular lipid metabolism; central nervous system development; endocytosis; nervous system development; neurogenesis; nucleocytoplasmic transport; organelle organization and biogenesis; phosphate metabolism; protein kinase cascade; response to endogenous stimulus; Rho protein signal transduction; small GTPase mediated signal transduction; synaptic transmission; transcription from RNA polymerase II promoter; transmembrane receptor protein tyrosine kinase signaling pathway; ubiquitin cycle; vesicle-mediated transport
SRF	N/A
SRY	Cell adhesion; cellular process; intracellular signaling cascade; mRNA processing; organic acid metabolism; response to DNA damage stimulus; RNA metabolism; RNA splicing; steroid metabolism
TBP	Protein transport; establishment of protein localization; RNA processing
TFIII*	Cell adhesion; cell differentiation; cell organization and biogenesis; chromatin modification; enzyme linked receptor protein signaling pathway; intracellular signaling cascade; nervous system development; organ development; protein kinase cascade; protein modification; transcription, DNA-dependent [54]
XVENT1	Cell cycle; cell growth; cell proliferation; cellular biosynthesis; establishment of cellular localization; inflammatory response; innate immune response; intracellular signaling cascade; lipid metabolism; mitochondrion organization and biogenesis; protein complex assembly; protein kinase cascade; response to endogenous stimulus; response to oxidative stress; RNA processing; RNA splicing; secretion; transcription from RNA polymerase II promoter
ZF5*	Actin polymerization and/or depolymerization; cell cycle; cell proliferation; cellular lipid metabolism; endocytosis; enzyme linked receptor protein signaling pathway; endoplasmic reticulum to Golgi vesicle-mediated transport; glycoprotein biosynthesis; hexose metabolism; induction of programmed cell death [47]; intracellular signaling cascade; JNK cascade; MAPKKK cascade; neurogenesis; phospholipid biosynthesis; protein amino acid glycosylation; protein kinase cascade; RNA splicing, via transesterification reactions; small GTPase mediated signal transduction; stress-activated protein kinase signaling pathway; ubiquitin cycle; vesicle-mediated transport; transcription from RNA polymerase II promoter [48]
ZIC3*	Cell adhesion; cell cycle; apoptosis; cell proliferation; cell-cell signaling; chromatin modification; cytoskeleton organization and biogenesis; development [56]; endocytosis; enzyme linked receptor protein signaling pathway; hexose metabolism; MAPKKK cascade; nervous system development; neurogenesis [55]; protein kinase cascade; small GTPase mediated signal transduction; striated muscle development; transmembrane receptor protein tyrosine kinase signaling pathway; vesicle-mediated transport

*TFs have corresponding functions proven by experiments from previous studies. N/A stands for no enriched or conserved biological function categories from this study.
Hu et al. Genome Biology 2007 8:R257 doi:10.1186/gb-2007-8-12-r257

Table 3