Beyond microarrays: Finding key transcription factors controlling signal transduction pathways

BMC Bioinformatics

Table 3 Key transcription factors found by pathway analysis of TNFα expression data. Transcription factors found by the downstream key node search starting from 129 signal pathway molecules whose expression has been changed more than 2-fold in primary human endothelial cells upon TNFα stimulation. (requires some explanation of the parameters shown here) Ni - number od relevant reachable molecules from the key node; Mi - number of non-relevant reachable molecules from the key node; Si - specifically score (see equation (3)).

TRANSPATH^® molecule acc	TF name	N _i	M _i	s _i
MO000018096	MEF-2C	80	1520	67.48
MO000020766	MEF-2°	71	557	66.48
MO000020759	NF-AT2	82	2040	65.65
MO000016887	STAT1alpha	89	2920	65.61
MO000000279	c-Fos	83	2202	65.42
MO000017496	FOXO3	74	1292	63.92
MO000013133	STAT5B	84	2578	63.89
MO000033504	PPAR-alpha	73	1218	63.55
MO000013122	STAT3	94	3946	63.44
MO000037096	MITF	78	1955	62.97
MO000019430	ER	72	1357	61.77
MO000017189	CREB	86	3223	61.72
MO000000038	Elk-1	80	2427	61.72
MO000038332	IkappaB-alpha, IkappaB-beta	87	3562	60.64
MO000045008	FOXO3, FOXO4	78	2350	60.61
MO000017212	NF-AT	82	2906	60.53
MO000044995	FOXO	78	2370	60.5
MO000013119	STAT1	87	3600	60.44
MO000022492	PPAR-gamma	77	2269	60.3
MO000017515	E2F	72	1638	60
MO000013126	STAT5A	82	3035	59.83
MO000000062	ATF-2	73	1818	59.74
MO000016628	SAP-1	77	2407	59.51
MO000000059	SRF	80	2885	59.16
MO000016876	STAT5	84	3521	58.75
MO000018995	RXR-alpha	77	2551	58.72
MO000034151	HIF-1alpha	78	2762	58.33
MO000045358	YY1:p53	71	1879	57.75
MO000017658	Smad2	82	3513	57.39
MO000000049	c-Jun	82	3622	56.86
MO000000058	NF-kappaB	77	3132	55.7

ISSN: 1471-2105