A structure-based Multiple-Instance Learning approach to predicting in vitrotranscription factor-DNA interaction

Gao, Zhen; Ruan, Jianhua

doi:10.1186/1471-2164-16-S4-S3

Table 2 Occurrence of ten most frequent high-scoring 7-mers in positive probe sequences for each TF (only 7-mers with a predicted probability of binding > 0.85 are considered.)

From: A structure-based Multiple-Instance Learning approach to predicting in vitrotranscription factor-DNA interaction

Cebpb		Esr1		Foxo1		Foxo4		Foxp2
GATTGCA	48	AGTCAAG	9	ACAAACA	53	GATAAAC	30	TGTATAC	32
TGTTGCA	43	ATGATCT	7	TGTTATT	52	AATAAAC	29	TGTTGTA	21
TATTGCG	42	ACGTCGA	6	TGTTTTT	47	CTATTTA	27	TGTGTAC	20
CATTGCA	39	ACGTTCT	5	TGTTTGT	44	AATAAAT	23	CTTGATA	12
CATTGCG	38	AGGTGCA	4	ACAACAT	41	CATAAAC	22	AATATCC	10
GATTGCG	35	ATGTTCT	4	TGTTGAT	41	GATAAAT	21	TGTGCTT	10
TTTTGCA	35	ACGATAT	3	TGTTATC	32	CATAAAT	19	TCTGTTC	10
CGTTGCA	33	AGTCAGC	3	ACAATAA	31	CTATTTG	11	ACTATCC	9
TTGCGAA	26	ACGCCCT	2	AAACAGG	21	GTATTTC	7	ATTATCC	9
Total	339	Total	43	Total	362	Total	189	Total	133
Irf2		Mecp2		Pou3f1		Sp1		Tcf3
TTTCATT	58	CACACAG	24	TTAATTA	62	TCCGCCC	38	CACCTGG	60
TTTCGAT	56	ACACAGG	24	CTAATTA	60	ACCGCCC	35	CACCTGA	43
TTTCGGT	56	GACACAG	17	ATTAATT	57	TGGGCGG	30	TCAGCTG	16
TTTCGCT	54	ACACAGC	15	GTAATTA	53	GCCGCCC	26	GAATGCA	13
TTTCACT	53	TACACAG	13	ATTAATA	50	GGGCGGG	23	CACCAGG	8
TTTCAGT	46	ACACGCT	13	ATTAATG	46	TACTCCA	14	TCGTCAC	7
TTTTCGT	46	ACACGGC	13	TATAATT	43	TCTGGGC	11	CACCAGA	5
TTTCTAT	43	TAAAGTA	10	ATTATTA	42	TGGGAGG	11	GCCAGAA	3
TTTTCAT	41	CACTGAC	9	AATAATT	40	GGGAGGG	10	TCAGCTT	3
Total	453	Total	138	Total	453	Total	198	Total	158
Egr2		Foxo3		Gmeb2		Nr2c1		Tbx3
CACCCAC	60	GCTGTTT	22	GTACGTA	68	ATGACCC	61	TAGGTGT	32
CTCCCAC	56	CTTATTT	21	TGACGTA	65	GTGACCC	60	AAGGTGT	30
GGCCCAC	47	AATATTT	20	GACGTAA	63	TTGACCC	60	CAGGTGT	23
AGCCCAC	43	GTTATTT	20	TACGTAC	63	TTGACCT	60	AGGGTGT	17
TACCCAC	42	CGTATTT	19	TTACGTC	60	GTGACCT	57	TGGGTGT	16
ATCCCAC	39	TCTATTT	19	CTACGTA	59	ATGACCT	45	GAGGTGC	15
TTCCCAC	27	ATTATTT	18	TACGTCA	53	CTGACCT	41	TCATCAC	13
AACCCAC	26	CCTGTTT	17	CGACGCA	51	TGACCCT	41	CTCACCT	12
GTCCCAC	23	TATATTT	17	TGACGTT	51	CTGACCC	31	CGGGTGT	12
Total	363	Total	173	Total	533	Total	456	Total	170
Foxj2		Foxp1		Junb		Sox14		Zscan20
ATGTTTA	48	CGTAAAC	32	TGCCACA	12	CAATTCA	34	AGGGTTT	20
AACAAAC	44	GGTAAAC	30	AGAATTC	12	CAATTGA	30	AGGGTCG	16
GTGTTTA	41	AGTAAAC	28	AATCTTT	11	CAATAGT	26	AGGGTTG	14
AACAAAT	35	TGTAAAT	27	GTCAACA	10	CAATAAA	24	TACAGGT	14
TTGTTTT	35	AGTAAAT	23	ACGTTCC	8	CAATGTA	24	AGGGTCA	10
TTGTTTG	30	CGTAAAT	18	GTCCGTA	7	CAATAAC	22	AACTCTG	10
AACAAAA	28	ACTAAAC	17	TTGCGCT	7	CAATTAC	22	AGGGTCT	9
AACAAAG	28	CAACAGG	15	CGCCACA	7	CAATACT	21	GTAAGGT	9
TACAAAC	28	GGTAAAT	15	GCCGTAC	6	CAATACA	19	ACAATAG	8
Total	317	Total	205	Total	80	Total	222	Total	110

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ISSN: 1471-2164

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