. Author manuscript; available in PMC: 2018 Jun 13.

Published in final edited form as: Genes Chromosomes Cancer. 2015 Jul 14;54(9):527–541. doi: 10.1002/gcc.22265

TABLE 3.

Networks Associated with CIMP High Tumors the Differentially Expressed Genes in our Data [Color table can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

ID	Molecules in network	Score	Focus molecules^a	Top diseases and functions
1	$AGR2,$ Alpha catenin, ANO1, AQP5, ATP9A, $AXIN2, B3GALT5, CDX2,$ Cg, $CREB3L1, DAPK1, DUSP4, ELAVL2, EREG,$ ERK1/2, FSH, GUCY2C, $KCTD1, LGALS2,$ Lh, $MSI1, MT2A, MUC5B, NKD1, PDE4D, PITX2, PLK2,$ Proinsulin, $PYY, RPRM, SOX1, TDGF1, WIF1,$ Wnt, $ZIC2$	54	24	Organismal development, cellular development, cellular growth and proliferation
2	ADCY, AMPK, Calmodulin, Creb, $DRD5,$ F Actin, $FFAR4,$ GHRHR, GLP1R, Gpcr, $GPR132, GPR143,$ GPR160, GRM8, Jnk, $MFSD4, MLPH,$ PARP, $PHACTR3,$ PI3K (complex), Pka, Pkc(s), PP1 protein complex group, $PPP1R14C, RAB27B, RAB3B, RAMP1, SLC14A2, SLC38A3, SLC39A4, SLC39A12, SLC6A4,$ SNCAIP, $SPDEF,$ VEGF	37	18	Cell signaling, molecular transport, nucleic acid metabolism
3	ACE2, Akt, Alp, AMACR, ASCL2, CEACAM6, Collagen(s), CTTNBP2, DDC, $DPEP1,$ ELOVL5, $ESRRG,$ Growth hormone, HDL, HDL-cholesterol, hemoglobin, Histone h4, IL1, Laminin, LDL, LDL-cholesterol, $LPL,$ N-cor, $OPTC, PMEPA1,$ Ppp2c, $SERPINF2, SLC2A8, TFF1, TG,$ TGFB, $TINAG, TRPV6, VNN1, XPNPEP2$	33	13	Cell cycle, lipid metabolism, molecular transport
4	$ADRA2A,$ Ap1, ARID3A, BEX2, CD3, CDC42EP1, DLEU7, E2f, ERK, estrogen receptor, F7, IFI6, IFN Beta, INPP5D, $KCNK5, KIAA0226L, KRT13,$ Mapk, NFkB (complex), PDGF BB, PLA2, $PLA2G12B, PLA2G2A, POFUT1,$ Rac, $RARRES3,$ Ras, $RNF125, ROR1,$ Shc, Sos,TCR, $TNFRSF11A, VAV3, XAF1$	32	14	Cardiovascular disease, developmental disorder, cell-to-cell signaling and interaction
5	ADIRF, BSN, $CA8,$ CECR2, CENPB, DHX34, DNAJC13, ETV7, EXT2, FAM49A, FITM2, FZD5, $GALNT5, HOXC6, KRT13,$ $KRT23, L3MBTL1, LAPTM4B,$ MICAL1, $NKD2, PCMTD2, PLCB4,$ PLXDC1, $QSOX1,$ RNF25, $RNF43, RPS6KA6,$ SAP30BP, $SEMA5A,$ SPTBN4, SRSF5, $ST3GAL4,$ UBC, UFM1, ZSCAN2	27	15	Cellular assembly and organization, cellular development, cellular growth and proliferation
6	ACSL5, ATP9A, BARX2, Bmyo, CLDN4, COL6A2, COL6A3, CREB3, $DUSP4,$ FGF5, FGF12, GDPD5, GPCPD1, $GPR132,$ IL13, IL22RA2, KLK1, LIF, LPCAT3, $LY6G6C, MUC5B,$ MYL3, OSM, $PLAGL2, PLLP, QSOX1,$ SELE, $SLC30A2, SLC6A4,$ SPINT1, SRF, $ST6GALNAC6,$ TGFB1, $TMEM40, TPBG$	27	12	Hereditary disorder, skeletal and muscular disorders, antimicrobial response
7	ADK, $AK1,$ APP, BCKDK, CAB39L, CCDC144NL, CKMT1A/CKMT1B, CXXC1, ENO3, $ESRRG,$ FGF12, GSPT2, H2AFJ, H2AFY, HSP90AA1, LAMC1, MAST2, $MOGAT3, NOL4L,$ NSRP1, $PRR15, R3HDML, RPS6KA6, SLC13A3,$ SMG1, SMG5, $SMTNL2,$ SMYD3, SRPK1, STK26, STRADA, $TRIM7, TTI2, TTPA, UPF3A$	26	13	Molecular transport, DNA replication, recombination, and repair, nucleic acid metabolism
8	26s Proteasome,3,20-pregnanedione, $ABAT, ABCA3,$ AQP5, calpain, CAPN9, CAPN10, CAPN11, caspase, $CEBPA,$ CEL, CFTR, $CYP2B6, FAM3B,$ GAS2, GATA5, Histone h3, Hsp90, IL12 (complex), Immunoglobulin, Insulin, Interferon alpha, LST1, $MLPH, NR1I2, OXCT1,$ P38 MAPK, $PRAP1,$ RNA polymerase II, $SLC9A3, Sult2a2, TNNC2,$ Troponin C, Ubiquitin	25	11	Lipid metabolism, small molecule biochemistry, cell morphology
9	ADAM9, AKAP11, $ANO9,$ ATP2B2, CPNE9, DLG1, DLGAP4, EIF5AL1, $ELAVL2,$ ENGASE, FZD4, GAS1, GLI1, GUCY1A2, $MAP7D2,$ MARCH2, MPP1, MPP2, PAPSS2, PHLDA2, $PLD5,$ PLOD1, RAB34, $REG4,$ RNASEL, $SDR42E1,$ SULF2, $SVOPL,$ UBC, $ZIC2, ZNF529, ZNF737, ZNF773, ZNF813, ZNF518B$	25	13	Nucleic acid metabolism, small molecule biochemistry, embryonic development
10	$B3GNT7,$ DLX1, DUSP5, EED, ELAVL1, ETF1, EVX1, FAM217B, FARP1, FOXE1, $HOXB13,$ IYD, $LRRC2,$ Macf1, MBD3, MGA, NCKAP1, NFIB, $NKD1, NR6A1,$ PEG3, POU5F1, PPHLN1, RBM15, $REC114, SLC16A14, SPIN3,$ TBX3, $TC2N,$ TEAD2, $TP53RK, UNC45B,$ WNT8B, $ZIC2, ZSWIM1$	23	13	Gene expression, embryonic development, organismal development
11	ALDOC, BAG3, CACNA1G, CACNG4, CEND1, CTNNBL1, DDX27, DKK3, dopamine, $DRD5, EPDR1,$ ERP27, GABRG2, GNG3, $GNG4,$ GNG7, GNG12, GNG13, HTT, KCNK2, $KRT38, MOCS3,$ NCKAP1, $OC90,$ OPRK1, $PGBD5,$ SPP1, SYN2, $SYN3, TMEM252,$ UBD, UBQLN4, UCHL3, YWHAG, $ZMYND8$	20	10	Neurological disease, cell-to-cell signaling and interaction, drug metabolism

Focus molecules are those significantly differentially expressed with CIMP high tumors in our data. Red font indicates upregulated genes, while green font indicates down-regulated genes.