Table 4.

Top Scoring Promoter Phylogenetic Motifs identified in Coding and Non-coding Strands. Top 1% and 5% Gene Sets.

Rank	Phylogenetic Motif	Known Factor	Position Bias*	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	TCAnnTGAY	SREBP-1	-64	68	70	44	103	0.0010	0.1794
2	TAATTA	CHX10	-	70	68	46	101	0.0011	0.1895
3	RnTCAnnRnnYnATTW	-	-	15	123	3	144	0.0027	0.4563
4	CATTGTYY	SOX-9	-	30	108	13	134	0.0027	0.4690
5	CTTTGA	LEF1	-	83	55	64	83	0.0063	1
	Top 1% Known Morifs Noncoding Strand
1	CAGnYGKnAAA	-	-	19	119	3	144	0.0002	0.0373
2	TAATTA	CHX10	-	70	68	46	101	0.0011	0.1895
3	TTAnWnAnTGGM	-	-	14	124	2	145	0.0014	0.2349
4	TTGTTT	FOXO4	-	98	40	79	68	0.0033	0.5672
5	YYCATTCAWW	POU1F1(*)	-	21	117	7	140	0.0046	0.7760
	Top 1% Known Morifs Coding & Noncoding Strand
1	TAATTA	CHX10	-	70	68	46	101	0.0011	0.1906
2	CAGnYGKnAAA	-	-	26	112	9	138	0.0011	0.1918
3	TAAWWATAG	RSRFC4	-	31	107	14	133	0.0033	0.5631
4	TTGTTT	FOXO4	-	121	17	116	31	0.0574	1
5	CATTGTYY	SOX-9	-	45	93	27	120	0.0064	1
	Top 5% Known Motifs Coding Strand
1	CTTTAAR	-	-	329	406	282	484	0.0019	0.3351
2	YKACATTT	-	-	174	561	133	633	0.0026	0.4526
3	TAATTA	CHX10	-	341	394	301	465	0.0057	0.9801
4	YATTnATC	CDP(*)	-	183	552	147	619	0.0088	1
5	TTGCWCAAY	C/EBPBETA	-	15	720	34	732	0.0090	1
	Top 5% Known Morifs Noncoding Strand
1	WTGAAAT	-	-	307	428	263	503	0.0034	0.5955
2	TTGTTT	FOXO4	-	491	244	456	310	0.0039	0.6670
3	TAATTA	CHX10	-	341	394	301	465	0.0057	0.9801
4	YCATTAA	IPF1(*)	-	204	531	166	600	0.0070	1
5	TTAYRTAA	E4BP4	-	129	606	97	669	0.0093	1
	Top 5% Known Morifs Coding & Noncoding Strand
1	TGCCAAR	NF-1	-	442	293	394	372	0.0007	0.1271
2	YCATTAA	IPF1(*)	-	326	409	282	484	0.0032	0.5575
3	YATGnWAAT	OCT-X	-	250	485	209	557	0.0051	0.8729
4	TAATTA	CHX10	-	341	394	301	465	0.0057	0.9744
5	AACYnnnnTTCCS	-	-53	76	659	49	717	0.0066	1

*Center of motif relative to transcriptional start site