Table 3

Functional comparison of SMAD responsive (from gene expression) and SMAD-target (from ChIP-chip) gene sets obtained using Ingenuity Core analyses

IPA Signaling Pathway

Affymetrix (1095 genes)

SMAD predicted (150 targets)


IPA ratio

IPA p-value

No. molecules

IPA ratio

IPA molecules


TGF-beta signaling

0.169

3.68E-06

14

0.012

SMAD3


RAR activation

0.08

2.50E-03

15

0.011

GTF2H2, SMAD3


IGF-1 signaling

0.108

3.58E-03

10

n/a

n/a


Wnt/beta-catenin signaling

0.084

4.12E-03

14

0.018

CSNK1A1, DKK1, FRAT1


Cell cycle: G1/S checkpoint regulation

0.117

7.37E-03

7

0.033

HDAC9, SMAD3


BMP signaling

0.097

1.01E-02

10

n/a

n/a


GM-CSF signaling

0.113

1.34E-02

7

0.016

CAMK2D


LPS/IL-1 mediated inhibition of RXR function

0.065

2.68E-02

13

n/a

n/a


IL-4 signaling

0.1

5.15E-02

7

0.014

NFAT5


Only significant signaling pathways are listed. Ratio shows the relative overlap between number of molecules per pathway within each dataset over the total number of pathway-specific molecules present in Ingenuity Knowledge Base.

Qin et al. BMC Systems Biology 2009 3:73   doi:10.1186/1752-0509-3-73

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