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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
  1. 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].
  2. NS: Not significant at p < 0.05. #Genes tested in each case: 20700.