Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation

Table 3 Top Scoring Promoter TFBS Motifs Identified in Coding and Non-coding Strands. Top 1% and 5% Gene Sets.

Rank	Known Motif	Factor	Genes with Motif	Genes w/o Motif	Genes with Motif	Genes w/o Motif	Fisher Raw p-value	Hochberg adj p-value
			Genes Overexpressed in ER+ Tumors		Genes Overexpressed in ER- Tumors
	Top 1% Known Motifs Coding Strand
1	CTTTGA	LEF1	83	55	64	83	0.0063	0.7784
2	TATAAATW	TBP	32	106	17	130	0.0117	1
3	MGGAWGT	PEA3	72	66	55	92	0.0128	1
4	TnGCGTG	AHR	39	99	23	124	0.0142	1
5	WADTAAWTA	NKX6-2	53	85	36	111	0.0149	1
	Top 1% Known Motifs Noncoding Strand
1	ABWCAGGTRnR	AREB6	13	125	2	145	0.0026	0.3205
2	KTWGTTT	SRY	91	47	71	76	0.0029	0.3487
3	ATTGTT	SOX-5	77	61	56	91	0.0030	0.3683
4	GCGCSAAA	E2F	0	138	8	139	0.0073	0.8725
5	RnCAGGTG	MYOD	68	70	50	97	0.0114	1
	Top 1% Known Motifs Coding & Noncoding Strand
1	ABWCAGGTRnR	AREB6	25	113	6	141	0.0002	0.0240
2	CTTTGA	LEF1	108	30	96	51	0.0180	1
3	KTWGTTT	SRY	120	18	110	37	0.0107	1
4	ATTGTT	SOX-5	100	38	93	54	0.1014	1
5	RWAAACAA	FOXO1	96	42	83	64	0.0272	1
	Top 5% Known Motifs Coding Strand
1	SCACGTG	MYC	141	594	190	576	0.0089	1
2	GnCnGTT	MYB	590	145	579	187	0.0296	1
3	RTGACTCAGCA	NF-E2	0	735	6	760	0.0311	1
4	MGGAWGT	PEA3	358	377	332	434	0.0384	1
5	KTWGTTT	SRY	473	262	454	312	0.0437	1
	Top 5% Known Motifs Noncoding Strand
1	KTWGTTT	SRY	473	262	423	343	0.0003	0.0422
2	GCGCSAAA	E2F	13	722	31	735	0.0092	1
3	CYAATTWT	HOXA4	306	429	271	495	0.0146	1
4	TYAAGTG	NKX2-5	276	459	242	524	0.0168	1
5	GCCATnTT	YY1	168	567	137	629	0.0176	1
	Top 5% Known Motifs Coding & Noncoding Strand
1	KTWGTTT	SRY	613	122	606	160	0.0346	1
2	WGATAR	GATA	691	44	698	68	0.0388	1
3	TYAAGTG	NKX2-5	450	285	420	346	0.0139	1
4	CCGGAART	ELK-1	97	638	69	697	0.0106	1
5	GTTRCYWnGYnAC	RFX1	12	723	4	762	0.0441	1

ISSN: 1471-2105