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.