Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction

EURASIP Journal on Advances in Signal Processing

Table 3 Transcription factors used in this study. "1" and "2" each represents that the corresponding TF binds to DNA in a single and double strand manner, respectively. Empty blank means no literature information is found.

TF	Prediction	Literature	Recognition sequence
AP1	1	1 [22]	GCTCCTCCCA, ATTAATCA,
			CCCGGGCGTGACTG, TGCGTCA
AP2A	2	2 [23]	GCCGGAGG, CCGCCGGGGTGG, CCCAGGG
CEBPB	2		AATGGCAAT
E2F	2		(CC)TTTCGCGC
EGR1	2	2 [24]	GCGGGGG(CG), TCCCCCCTGCCCCGCCGGGCCCCGCCC
GATA4	2		AGATAG, TGAGATTACA
HNF3	1		AAGTCAATAATC(A), TTTGTGTAGGTTA
IPF1	1		TCTAAT
MEF1	2		CCCCCCAACACCTGCTGCCTGAGCC
MEF2C	1		CTATAAATAC
MYB	2		GAACGT, ACGTTA
MYF5	2	2 [25, 26]	CCCAACACCTGCTGCCTGAGCC, CATCTG, CAGTTG
MYOD1	2	2 [25, 26]	CAACTG, (ATTAACCCA)GACATGTGGC(TGCCCC), CATCTG,
			(CCCCCCAA)CACCTGCTG(CCTGAGCC), CACTTG, CAGTTG
MYOG	2	2 [25, 26]	(C)CCCAACACCTGCTGCCTGAGCC, CATCTG, CAGTTG
NFAT	1		TTTCCTC
NFKB1	2		GGAGATTCCAC, CCACAACTCA
NFYA	1		CAAT
SP1	2	2 [27]	(T)TCGGGGCGGTGT(G), GCCCCCCAC(CCCTGCCCC),
			CCGCCC, CCCCACCCCCTGCA, GCGCCAGGGCTGGGCTCCT,
			CACCTTGGCCACGCCCCTTTGG, CCTGCTTCCCGCCTTTCG,
			TTTGGTTCCCGCCTCCCCGCCCCC, CCCCTCC(C),
			TCCTGAAGACCCGCCCTTTTTC, GGCAGAG, CAACC,
			GGGCGGGGCCGTGGCTCC, GAGCGTGGCGGGCCGCG,
			(AGGG)TGGGCAG(TCC), GAGGTGGGGGG, AGCCAG,
			(GGGGGGGGGGGGGGGG)GGGCGG(GGCCGTGGCT),
			(CCTAAAGTGCTTCCAAA)CTTGGCAAGGGCGAGAGAGGGCGGGTGG
SRF	1		ACCCAAATATGGCT, CCTTACATGG,
			CCAAGAATGG, CCAAATAAGG,
			GCCCATGTAAGGAG, GAAACGCCATATAAGGAGCAGG,
			GCAGCGCCTTATATGGAGTGGC, CTCCAAATTTAGGC,
			TGCTTCCCATATATGGCCATGT, CCATATTAGG, CTATTATGG
TBP	1		(C)TATAAA(A), TACAAAT, TTAAA,
			ATAAATA, TTAAAT, TATAAG
TCF1	1		GTTATTGGTTAAAGAAGTATA,
			GTGTAGGTTACTTATTCTCCTTTTGTTGA
TEAD1	2		(AA)CATTCCTT(CGG), AGGAGGAATGTGC
TRP53	2		GAGCAAGTCA, ATACAAGGCC