Systematic target function annotation of human transcription factors

Table 1 Top 20 TF-target disease associations. The “Literature Rich” gene universe is used for the association detection

TF	Target disease	log₂(OR)^a	P value^b	Evidence^c
ATF3	Lysosomal storage disease	4.5	3.9 × 10^-09	–
BRCA1	Mitochondrial metabolism disease	3.1	3.7 × 10^-09	–
CTBP2	Heart septal defect	6.9	4.4 × 10^-10	Mouse^f [149]
CTBP2	Congenital heart disease	6.5	1.6 × 10^-09	Mouse^f [149]
ETS1	Organ system cancer	2.6	1.2 × 10^-08	Mutation^d [150]
GATA1	Acute porphyria	7.4	9.8 × 10^-09	Mutation^d [50]
HNF4A	Mitochondrial metabolism disease	3.0	5.3 × 10^-09	Mutation in MODY1^d [140]
NFE2	Lysosomal storage disease	5.7	4.8 × 10^-12	–
NFE2	Lipid storage disease	6.0	5.8 × 10^-09	–
RFX2	Bardet-Biedl syndrome	5.5	1.1 × 10^-12	Mouse^f [144, 145]
SOX10	Waardenburg’s syndrome	11.4	2.0 × 10^-09	Mutation^d [141]
SUZ12	Heart septal defect	6.2	7.4 × 10^-09	Mouse^f [151]
TP53	Organ system cancer	3.5	1.5 × 10^-19	Mutations in multiple cancer^d
	Cancer	3.5	3.6 × 10^-19	Types [152]
	Disease of cellular proliferation	3.4	1.7 × 10^-18
	Reproductive organ cancer	4.8	1.2 × 10^-08
USF1	Disease of metabolism	2.2	1.3 × 10^-10	Association with FCHL^e [153, 154]
USF1	Inherited metabolic disorder	2.2	7.5 × 10^-09	Association with FCHL^e [153, 154]
USF2	Lysosomal storage disease	4.1	1.3 × 10^-09	–
USF2	Disease of metabolism	2.3	2.8 × 10^-09	–

^alog2(OR), log2 transformed odds ratio
^bP value from single-tailed Fisher’s exact test for odds ratio > 1
^cEvidence lists published genetic evidence directly support the association of the TF with the disease
^dMutation mutations of the TF are observed in the disease or closely related diseases
^eAssociation, the TF gene locus is genetically associated with the disease or related diseases
^fMouse mouse model shows phenotypes directly related to the disease.
Non-genetic evidence in the literature is not considered.
MODY1 maturity-onset diabetes of the young, FCHL familial combined hyperlipidemia

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