. 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 4.

Networks Associated with MSI Differentially Expressed Tumors [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	$AGR2,$ $AKAP5,$ Alpha catenin, $ATOH1, ATP9A,$ AXIN2,Cg, Creb, $CREB3L1,$ $DUSP4, EREG, ERK1 / 2, FSH, GNLY, HOXB13,$ Lh, $LRRN1, MT1X, MT2A, MUC2,$ MUC4, $MUC5AC, MUC5B,$ Mucin, $NKD1, NR6A1, PDE4D, PITX2, PYY,$ RAP1GAP, $RPRM,$ SOX1, $T, TDGF1,$ Wnt	55	26	Cell death and survival, cell morphology, organ morphology
2	$ADRA2A, ASCL2,$ caspase,CD3, $CEL, DLEU7,$ ERK, F7, F Actin, FABP6, $FAM46A, FFAR4, FRAS1,$ FREM1, $FREM2,$ Gpcr, $GPR143, GPR157, GRM8, GTF2IRD1,$ Histone h3, Jnk, $KIAA0226L, LRRC2,$ Mapk, NFkB (complex), $NUDT6,$ PI3K (complex), Pka, Pkc(s), $POFUT1, SPDEF, TPH1,$ VEGF, $XAF1$	39	20	Developmental disorder, hereditary disorder, ophthalmic disease
3	$ABAT,$ $ABCA3,$ DCY, Akt, Ap1, $ARID3A, CEBPA,$ CYP27A1, $CYP2B6, DDC, DGAT2, DPEP1,$ E2f, $FAM3B,$ HDL, IL1, Immunoglobulin, Insulin, $IP6K3,$ LDL, $LPL, MLPH,$ Nr1h, $PLA2G2A, PMEPA1, PRAP1, RAB27B,$ Ras, $REN, SALL4, SERPINE2,$ Sos, Tgfbeta, $TNFRSF11A,$ trypsin	38	20	Cell morphology, cellular assembly and organization, tissue morphology
4	ADK, $AGR2,$ APP, ARID3B, $B3GNT7,$ CHMP3, COL4A6, CST3, $CTTNBP2, CXCL14, DUSP4,$ EXT2, FBXO38, FXYD1, GBP4, $GDPD5, HYPK, KLF7,$ Macf1, miR-224-5p (miRNAs w/seed AAGUCAC), MYH9, $MYOM3, PKNOX1, PLAGL2,$ plasminogen activator, POU5F1, PPP2CA, $PRR15, PTPRO,$ SELE, SMCHD1, $SMTNL2,$ ST6GALNAC6, STRIP2, TGFB1	24	15	Cardiovascular disease, developmental disorder, hereditary disorder
5	ADK, $AK1,$ ARIH1, $CAB39L,$ CLCN5, dopamine, FARP1, GGT7, HECW1, KCTD20, KIF3C, $KRT23, MAPRE3, MARK1, NOL4L,$ NUDT2, $PALD1, PHACTR3,$ PPHLN1, PPP1CA, $RNF43,$ RNF19A, $SLC9A3, SNCAIP,$ SNCB, SRPK1, STK11IP, STRADA, STXBP2, $SYN3,$ SYT3, TROAP, UBC, USP48, $ZSWIM3$	23	14	Molecular transport, cell-to-cell signaling and interaction, nervous system development and function
6	12-hydroxyeicosatetraenoic acid, $APOLD1,$ $ARSJ,$ CELSR3, COL12A1, $COL9A1,$ COL9A2, $COL9A3,$ Collagen type ix, COMP, CYP4F2, FMOD, FN1, FZD8, G-protein gamma, $GNG4,$ GNG5, GNG7, GRB2, HNRNPA2B1, HSP90AA1, $HUNK, LY6G6F,$ MYRIP, NCK1, $NKD2,$ PHACTR2, $PLCB4,$ RAF1, $RNF125, SGSM2, SHROOM2, SLC22A3,$ STK32C, $TRIM7$	23	14	Connective tissue disorders, developmental disorder, hereditary disorder
7	$AMACR, AQP5,$ CATSPER1, CATSPER4, $CATSPERB, CTSE,$ CYP27A1, $DDX27,$ DMD, $EPDR1,$ Flg, FXYD1, GFER, HSPA2, $IGFN1,$ IL31, $IP6K3, LY6G6C,$ Mt3, nitrite, NR3C1, OSM, P38 MAPK, $PLLP,$ PPARA, $PPP1R14C,$ PPP1R16A, RBP4, SIRT1, SLC10A2, $SLC1A7, SNTB1,$ Stat3-Stat3, TLR5, $TNNC2$	23	14	Lipid metabolism, small molecule biochemistry, vitamin and mineral metabolism
8	$ABLIM2,$ ADH6, ADH1B, APCDD1, B3GALT1, $B3GALT5, CA8,$ CEBPB, COL4A5, Cyp2c11l, $CYP2W1,$ ELAVL1, F Actin, FOXJ3, GAS2, $GOLT1A,$ HNF1A, HNF4A, $KLHL3, MT1X,$ MTF2, PCNP, $PLA2G12B,$ Rbp, $SLC22A11,$ Sprr1b, $ST3GAL4, STRA6, TMEM176A,$ TNFRSF19, tretinoin, UGT2B7, UGT2B15, XPNPEP2, $ZNF556$	22	14	Cellular development, digestive system development and function, hepatic system development and function

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