. Author manuscript; available in PMC: 2013 Jan 1.

Published in final edited form as: Proteomics Clin Appl. 2011 Dec 27;6(1-2):117–133. doi: 10.1002/prca.201100083

Table 3.

Subnetworks over-represented in the 54 proteins

ID	Molecules in subnetwork	Score^a)	Number of focus molecules^b)	Top functions
1	ACTA1^c), ACTA2, ACTB, ACTC1, ACTG1, ACTG2, Actin, Alpha actin, Alpha Actinin, Alpha catenin, atypical protein kinase C, Cadherin, CASP1, CASP3, ERK1/2, Fgf, G-Actin, Hsp27, Hsp90, Ige, JUP, KAT5, OSBP, PFN1, Phosphatidylinositol4,5 kinase, Pld, PP2A, Profilin, RAB9A, Ras homolog, Rho gdi, RHOC, RhoGap, Rock, Rsk	29	14	Cell Death, Cellular Assembly and Organization, Skeletal and Muscular System Development and Function
2	14-3-3, Alcohol group acceptor phosphotransferase, BAG5, BCR, Caspase, CD3, Cdc2, CDC42, DSP, Ephb, EXOC7, F Actin, Fcer1, Filamin, FLNA, IQGAP, IQGAP1, KRT8, KRT18, Laminin, MAP2K4, MAP2K7, MAP2K4/7, MAP3K, Mek, NFkB (complex), Pak, Pkg, PKN1, Raf, Rap1, Sapk, TCR, TXN, VAV	24	12	Cellular Assembly and Organization, Gastrointestinal Disease, Genetic Disorder
3	26s Proteasome, AIP, Akt, APC/APC2, Calmodulin, Cbp/p300, Ck2, CTNNB1, DNAJB11, FSH, Gpcr, hCG, Histone h3, Histone h4, Hsp70, Ifn gamma, IgG, Ikb, IL12 (complex), Insulin, Interferon alpha, Jnk, Lh, Pka, PLC, PLS3, RNA polymerase II, TP53, UBB, UBC, UBE2D1, UBE2L3, Ubiquitin, VCP, YWHAG	20	11	Cancer, Cellular Development, Cellular Growth and Proliferation
4	AMPK, Ap1, Calpain, Collagen type I, Collagen type IV, ERK, Estrogen Receptor, Fibrinogen, Focal adhesion kinase, G protein beta gamma, Gef, IFN Beta, IL1, Integrin, LDL, Mapk, MAPK1, NFKBIA, P38 MAPK, p85 (pik3r), Pdgf (complex), PDGF BB, PI3 K (complex), Pkc(s), RAB5A, RAB7A, Rac, RAC1, Ras, RHOA, STAT5a/b, Tgf beta, TLN1, TRIP6, Vegf	14	8	Cardiovascular System Development and Function, Cell-To-Cell Signaling and Interaction, Cell Signaling
5	AFAP1L2, AGT, AKIRIN2, ARL6, ARL4C, BUB3, C11orf1, CAPRIN1, CES2, COX7A2, GIPC2, HNF4A, HNRNPA0, HOOK3, IL6, IRF6, LPP, MRPL44, NIPSNAP3A, POLR3G, PRCP, PTK2, PTK7, REG1A, SBNO2, SETDB1, SLC14A2, SLC16A6, SUGT1, TDO2, TXNDC9, UBA52, UTP3, XPNPEP2, ZFP64	10	6	Increased Levels of CRP^d), Cell Morphology, Cellular Development

^a)

Scores were log-transformed by the P-values, which were calculated by Fisher’s exact test.

^b)

The number of focus molecules is the number of the genes with the bold font.

^c)

The genes with the bold front are these genes existed in our gene set.

^d)

CRP is abbreviated for c-reactive protein.