Complex-based analysis of dysregulated cellular processes in cancer

Srihari, Sriganesh; Madhamshettiwar, Piyush B; Song, Sarah; Liu, Chao; Simpson, Peter T; Khanna, Kum Kum; Ragan, Mark A

doi:10.1186/1752-0509-8-S4-S1

BMC Systems Biology

Table 5 Influential TFs identified in pancreatic (normal vs PDAC) and breast (BRCA1 vs BRCA2) tumours.

From: Complex-based analysis of dysregulated cellular processes in cancer

Pancreatic						Breast
TF	γ	Norm- γ	#Complexes regulated	p -val	DE ( p -val)	TF	γ	Norm- γ	#Complexes regulated	p -val	DE ( p -val)
STAT5B	2.911	1.000	188	0.001	0.021↓	TBP	−5.153	−1.000	199	0.001	NS
RREB1	−2.606	−0.895	190	0.004	NS	BACH1	4.221	0.819	199	0.003	NS
BACH1	−1.592	−0.547	188	0.001	5.48E-05↑	POU3F2	−3.902	−0.757	199	0.007	NS
SRF	1.522	0.523	40	0.004	3.06E-05↓	RREB1	2.654	0.515	200	0.002	NS
IRF2	−1.462	−0.502	37	0.014	1.24E-06↓	ATF6	−1.185	−0.230	201	0.002	NS
AHR	1.359	0.467	190	0.003	1.93E-11↑	SRF	1.079	0.209	40	0.007	NS
TBP	−0.944	−0.324	188	0.002	0.001↑	STAT5B	1.022	0.198	199	0.007	NS
POU3F2	−0.731	−0.251	188	0.002	6.64E-07↓	SIN3A	0.980	0.190	205	0.007	NS
IRF7	−0.654	−0.225	188	0.002	2.50E-06↑	TCF4	0.601	0.117	40	0.007	NS
HSF1	−0.621	−0.213	190	0.001	NS	TAL1	0.599	0.116	14	0.007	NS
YY1	0.619	0.213	195	0.001	3.80E-05↑	CEBPβ	−0.537	−0.104	201	0.002	NS
STAT1	0.568	0.195	190	0.005	4.79E-06↑	SOX9	0.447	0.087	204	0.008	NS
TP53	0.543	0.187	190	0.004	6.34E-06↑	GATA3	0.422	0.082	90	0.001	0.012↑
XBP1	−0.549	−0.189	190	0.004	0.002↓	STAT1	0.411	0.080	202	0.001	NS
SOX9	0.504	0.173	193	0.004	2.43E-05↑	STAT5A	0.407	0.079	200	0.004	NS
CEBPβ	0.427	0.147	191	0.005	1.71E-08↑	NFκ B1	0.390	0.076	202	0.001	NS
ATF6	−0.419	−0.144	191	0.008	NS	IRF2	−0.389	−0.075	42	0.006	NS
STAT5A	0.385	0.132	188	0.001	0.004↑	GATA2	−0.323	−0.063	40	0.001	NS
MSX1	0.366	0.126	188	0.002	0.008↑	FOXO1	0.305	0.059	30	0.001	NS
GATA2	0.328	0.113	40	0.001	9.96E-03↓	ESR1	0.282	0.055	24	0.001	0.008↑
TAL1	0.319	0.110	12	0.003	1.09E-07↓	PPARγ	0.279	0.054	60	0.001	NS
FOXO1	−0.306	−0.105	30	0.003	0.001↑	TP53	0.273	0.053	206	NS	NS
ESR1	0.254	0.087	27	0.004	3.43E-04↑	YY1	0.274	0.053	206	0.009	NS
JUNB	0.219	0.075	198	0.004	2.44E-07↑	STAT3	−0.222	−0.043	200	0.004	NS
CEBPα	0.187	0.064	194	0.001	NS	MYB	−0.213	−0.041	60	0.003	NS
STAT3	0.169	0.058	190	0.004	2.34E-06↑	GATA1	0.204	0.040	40	0.001	NS
SP1	0.159	0.055	10	0.001	0.003↑	FOXA1	0.173	0.034	207	0.001	0.006↑
TCF3	0.155	0.053	40	0.001	NS	MSX1	0.170	0.033	199	NS	NS
BRCA1	0.146	0.050	200	0.003	0.003↑	HSF2	−0.165	−0.032	201	NS	NS
SIN3A	0.138	0.047	193	0.001	2.05E-4↑	FOXO3	0.147	0.029	50	0.009	NS
PPARγ	0.124	0.043	13	0.001	NS	PPARα	0.133	0.026	40	NS	NS
HSF2	0.120	0.041	191	0.001	0.004↑	FOS	0.121	0.023	44	0.005	NS
MAX	0.113	0.039	80	NS	N S	SP1	0.098	0.019	18	0.003	NS
NFκ B1	0.106	0.036	192	0.002	NS	TCF3	−0.096	−0.019	90	0.009	NS
FOS	0.044	0.015	42	0.001	NS	CEBPα	0.094	0.018	202	0.009	NS
MYB	−0.023	−0.008	40	0.002	NS	NFκ B2	−0.091	−0.018	202	0.003	NS
NFκ B2	0.018	0.006	193	0.002	NS	JUN	0.080	0.016	205	0.003	NS
FOXO3	−0.001	0.000	90	0.004	NS	AHR	0.076	0.015	200	NS	NS
-	-		-			XBP1	0.059	0.011	201	0.002	0.017↑
-	-		-			HSF1	−0.056	−0.011	200	0.001	NS
-	-		-			IRF7	−0.033	−0.006	199	0.009	NS

TFs are ranked based on their overall influence (|γ&pipe;) for normal vs PDAC and BRCA1 vs BRCA2 tumours. The normalized-γ values are obtained by dividing the γ values by the maximum |γ&pipe;. The significance (p value) was computed against 10000 background influence values, each generated from 10000 random shuffles of gene symbols in the expression dataset. The adjusted p-values for differential expression (DE) analysis - whether up- (↑) or down- (↓) regulated from normal to PDAC and from BRCA1 to BRCA2 tumours - were computed using limma [54].
NS: Not significant at p < 0.05. #Genes tested in each case: ∼ 20700.

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ISSN: 1752-0509

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