Differential Protein Network Analysis of the Immune Cell Lineage

Table 3

Common protein network exemplars.

Exemplar ID	Genes assigned to the protein network exemplar	Functional annotation	value
127	TANK, TNFRSF11A, TNFRSF4, TNFRSF9, TRAFD1, ZBP1	Cytokine-cytokine receptor interaction (KEGG)
32	ATP6V1A, BAIAP2, CAMK2D, CLU, DLG4, DYNLL1, EPS8, FZD1, FZD4, GRIA3, HCK, INADL, KCNJ10, NSF, OPRD1, PACSIN1, PACSIN2, PGK1, PHB2, PPP3CA, RGS12, SEMA4B, SEMA4C, SLC9A3R1, STXBP1, SYT1	Wnt signaling pathway (KEGG)
44	CD2AP, DAPK1, EFNA2, EPHA4, FGR, FYN, PKD2, RAVER1, RGS1, SH2D1A, SH3BP1, SLAMF1, VAV1, VAV2, ZAP70	T cell receptor signaling pathway (KEGG)
93	HNRNPA1, LGALS3, NCOA3, PIAS1, RNF19A	Transcription cofactor activity (GO_BP)
29	CLNK, FYB, LYN, PECAM1, SKAP2	Leukocyte activation (GO_BP)
62	CSF2RB, EIF2AK2, GHR, GMCL1, GNB2L1, HES1, IFNGR1, IL6ST, JAK1, JAK2, JAK3, LMO4, NCL, PAG1, SLC40A1	Jak-STAT signaling pathway (KEGG)
139	BRCA1, CIITA, GTF2H2, KDM5D, PDLIM4, POLR1A, POLR2B, TRIP4, TRPS1, ZFP111, ZFP292	Zinc ion binding (GO_BP)
135	RIPK2, TAX1BP1, TIFA, TNFAIP3, TNIP2	Apoptosis (GO_BP)
112	ANXA2, BMYC, GAB2, PRKCE, PRMT5, S100A10	Fc epsilon RI signaling pathway (KEGG)
140	CCNG1, CCNG2, E2F1, GSTA4, NR4A3, SWAP70, TRIM32, TRP53	Cell cycle (GO_BP)
124	HSPA5, HSPA9, HSPD1, PDXK, RAPGEF4, STIP1, YWHAE	Adenyl ribonucleotide binding (GO_MF)
79	ALDOA, CD40, IL1R1, IL1RAP, IL1RL1, IRAK3, IRAK4, IRF4, IRF5, LRRFIP1, MYD88, TIRAP, TLR4, TNFRSF13B, TUBA1A	Cytokine-mediated signaling pathway (GO_BP)
126	BCAR1, BLK, CD22, CD247, CLEC7A, ERBB2, IL15RA, ITGB3, RANBP2, SYK, TUBA4A, WIPF1	Cell surface receptor linked signal transduction (GO_BP)
21	CCL3, CCL4, CCR1, CCR3, CCR5	Chemokine signaling pathway (GO_BP)
63	APOE, CASK, CNN3, CTTN, HSP90B1, IPO11, KCNMA1, LDHA, MYO5A, NDEL1, NUDC, PRDX2, RAB6B, ROCK2, SH3BP4, TPM1, TPT1, TRF, TUBB5	Cellular homeostasis (GO_BP)
80	MYO1C, PCDH15, RICTOR, RRN3, VPS35	Cytoskeleton organization (GO_BP)
92	GFR, PDGFRA, PDGFRB, PTEN, SLC9A3R2	Transmembrane receptor protein tyrosine kinase signaling pathway (GO_BP)
142	CSNK1E, NXN, PLCG2, RAD51, VANGL1, VANGL2	Wnt signaling pathway (KEGG)
48	GRB10, IGF1R, MAP3K5	Insulin-like growth factor receptor signaling pathway (KEGG)
50	HCST, IL2RB, KLRK1, TYROBP	Integral to membrane (GO_BP)
52	ANP32A, DACH1, FOSB, HDAC2, HDAC9, L3MBTL2, MTA1, MTA3, RBBP7, REST, SP3, TCF7L2, WDR5, ZDHHC13, ZFPM1	Regulation of transcription (GO_BP)
116	F2RL2, MAP3K2, SMAD1, SMAD5, TOB1, ZEB2	Cell surface receptor linked signal transduction (GO_BP)
59	CASP1, CASP3, CASP8, CEBPB, GZMB, IL1B	Regulation of apoptosis (GO_BP)
46	E2F2, GATA1, GATA3, GFI1B, LMO2, NFYA	Transcription (GO_BP)
94	AXL, CD19, EPHA2, IL4RA, INSR, IRS2, KRAS, NEDD9, NME2, PDCD4, PIK3AP1, PIK3CA, PIK3CB, PIK3CD, PIK3R1, PLCG1, PTK2B, RALGDS, RASSF5, SIRPA, SOCS6, TEK, TLR2	Cell surface receptor linked signal transduction (GO_BP)