Table 1.

Significant gene networks significantly expressed below/above threshold, determined by SAM + IPA

Network	Score	“Hub” genes	Functions
1	24	Myc	Cellular transformation and proliferation
2	24	Bcl2, Ran	Apoptosis, RNA splicing, nucleocytoplasmic transport
3	24	Ccnd1 (Bcl1), Cul1	Stem cell factor ubiquitin ligase complex
4	24	Fn1	Cell adhesion
5	24	Egfr, small nuclear riboproteins	DNA synthesis, cell proliferation
6	24	Mapk7, Mapk14, Titf1	Cytokine production, transcription termination
7	24	Rb1	Tumor suppression, epigenetic transcriptional regulation, cell cycle control
8	24	H-Ras	Cellular transformation
9	24	Vim, Agt	Cell morphology and integrity
10	24	Il10, Chuk	Cytokine synthesis, modulation of NF-ÊÂ complex
11	24	Erbb2	Growth factor receptor production
12	24	NF-κβ ia, Tnfaip3, Ikbkg, Traf2	Cell adhesion, immune and proinflammatory responses, apoptosis, differentiation and growth
13	24	Crebbp, Ncoa2, Ncoa3	Nuclear receptor coactivation
14	24	Cepb, Eif*, Pabpc1	Regulation of immune/inflammatory responses, mRNA metabolism
15	24	Cdkn1b, Cops*, Eif*, Psmd1	Cell cycle arrest, regulation of transcription and ubiquitin ligase, proteasome
16	24	Bcl2l1, Cycs, Casp8/Casp9, Bax	Apoptosis
17	24	Egr1, Nr5a1, Fbl, Exosc	Proliferation, pre-RNA processing (exosome complex)
18	24	App, Nfatc1	T-cell activation, apoptosis, inhibition of notch signaling
19	24	Grb2, Rala, Sumo2, Ncl	Epidermal growth factor/platelet-derived growth factor signaling and Ras signaling, posttranslational modification, chromatin decondensation
20	24	Creb1, Sumo1, Hdac*	Histone deacetylation, transcription regulation
21	24	Prkar1a, Cox*, Gabpa, Icam1	Tumor suppression, mitochondrial structure, integrin binding
22	24	Tgfbr2, Smad1, Smad2, Smad3, Smad4, Mmp13	Tumor growth factor signaling, collagen degradation
23	24	Cdkn2a	Tumor suppression, G1–G2 cell cycle arrest
24	24	Igf2, Mcm2, Pcaf, Myst2/Myst4	Cell growth, DNA replication, histone acetylation
25	24	Il15, Polr*	Stimulation of T-cell proliferation, transcription
26	24	Epo, Jak1	Cytokine receptor signal transduction
27	24	Tpb, Smarc*	Transcription initiation, chromatin structure regulation
28	24	Itgam, Clec11a	Integrin adhesion, stimulation and proliferation of hematopoietic precursors
29	24	Myb, Sod1, Cdk4	Hematopoietic precursor proliferation, free radical destruction, G1-S cell cycle progression
30	24	Shh, Cd44, Fgf10	Proliferation signaling, cell differentiation
31	24	Irf1, Ifnb1, Isg15, Tnfrsf1b	IFN regulation and ubiquitination, apoptosis
32	24	Tra@, Cd247, Gata3, Parp1	T-cell receptor signaling, excision repair pathway
33	24	Rhoa, Gnaq, Plcb1, Gnb1	G protein signaling, focal adhesion point and actin fiber formation
34	24	Mdm2, Pax3	p53, Rb, E2F1 regulation, apoptosis
35	20	Ywhaz	Apoptosis, T-cell receptor signaling, histone modification

NOTE: For each network, prominent hub (highly connected) genes and cellular functions that are associated with the IPA network are listed. Network scores are −log(P value).