Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells

BMC Genomics

Table 5 Summary of expression fold change of predicted targets in the RAi data

Cluster	Feature	Cofactor	FC_RAi	N _b	N _e	P _c	1Q	Median	3Q
UH	E2f1.M00233_MEF2_04	Mef2a	N	198	191	0.90	1.67	2.28	4.64
UH	Sox2.M00974_SMAD_Q6_01	Smad2	H	92	90	0.89	1.82	3.01	8.50
UH	Sox2.M00974_SMAD_Q6_01	Smad4	H	92	90	0.89	1.82	3.01	8.50
UH	Esrrb.M00971_ETS_Q6	Elf2	H	150	144	0.92	1.62	2.32	4.12
UH	Esrrb.M00971_ETS_Q6	Gabpa	H	150	144	0.92	1.62	2.32	4.12
Oct4	Smad1.STAT3.M00052_NFKB	Rela	H	39	29	0.72	0.99	1.97	2.65
Oct4	Smad1.STAT3.M00415_ AREB6_04	Zeb1	N	36	25	0.76	1.16	1.83	2.65
Oct4	Tcfcp2l1.M00771_ETS_Q4	Elf2	H	90	82	0.82	1.16	1.97	4.15
Oct4	STAT3.M00251_XBP1_01	Xbp1	H	23	23	0.78	1.16	1.75	3.86
Oct4	Nanog.M00462_GATA6_01	Gata6	N	51	48	0.83	1.29	2.10	4.20
Oct4	Esrrb.N00007_SoxOctComp	Sox2 & Oct4	P	108	101	0.82	1.14	1.95	4.04
Oct4	Oct4.M00801_CREB_Q3	Atf1	P	45	40	0.75	1.00	1.91	4.41
Myc	M00233_MEF2_04	Mef2a	N	170	163	0.90	1.33	1.66	2.53
Myc	M00971_ETS_Q6	Gabpa	H	173	167	0.89	1.33	1.70	2.67
Myc	M00971_ETS_Q6	Elf2	H	173	167	0.89	1.33	1.70	2.67
Myc	N00003_Otx2	Otx2	P	166	160	0.90	1.34	1.67	2.59
Myc	M00034_P53_01	Trp53	P	166	160	0.91	1.34	1.67	2.71
Myc	M00512_PPARG_01	Pparg	N	167	160	0.89	1.34	1.70	2.59
Myc	N00009_Klf4	Klf2	P	184	177	0.89	1.33	1.68	2.58
Myc	N00009_Klf4	Klf5	P	184	177	0.89	1.33	1.68	2.58
Myc	M00422_FOX J2_01	Foxj2	N	168	161	0.90	1.34	1.70	2.58
Myc	M00724_HNF3ALPHA_Q6	Foxa1	N	177	170	0.89	1.32	1.67	2.46
Myc	M01011_HNF1_Q6_01	Hnf1b	N	180	174	0.89	1.34	1.67	2.48
Myc	Myc.M00480_LUN101	Topors	H	73	69	0.81	1.15	1.60	2.26
Myc	Mycn.M00931_SP1Q6_01	Sp1	H	80	78	0.73	0.95	1.43	2.16
Myc	Mycn.N00017_hB_Sall4	Sall4	P	87	82	0.74	0.98	1.57	2.60
Oct4-M	M01111_RBPJK_Q4	Rbpj	P	62	57	0.61	0.70	1.27	2.23
Oct4-M	M00450_ZIC3_01	Zic3	P	43	41	0.63	0.80	1.28	2.23
Oct4-M	N00001_Sox2	Sox2	P	49	46	0.57	0.70	1.09	1.45
Oct4-M	M00225_STAT3_01	Stat3	H	44	43	0.67	0.84	1.28	1.79

Note: FC_RAi is fold change of cofactor expression. N_b is the number of predicted targets for a feature. N_eis the number of targets having expression available in [9]. P_cis the proportion of N_egenes with expected expression change. 1Q, Median, and 3Q are, respectively, the 1st quartile, the median, and the 3rd quartile of targets' fold change, which is inverted for ES-down features for convenient comparison.

ISSN: 1471-2164