Table 2. Top three IPA-generated networks of differentially expressed molecules identified by DIGE and iTRAQ labeling between early and mock, late and mock, and late and early WNV-infected brain samples.

Top Functions	Score	Focus Molecules	Molecules in Network
Early vs mock
Protein Synthesis, Cell Death, Cancer	49	23	up-regulatedACO2 (includes EG:11429), GFAP, HNRNPA2B1, HP, HSP90AB1, METAP2, PGK1, PRUNE, STAT1, STAT2, TAPBPdown-regulatedALB, ARL8B, ATP5B, CAMK4, CSNK2A1, HBB, HSPA8, PPID, RNA RPS21, SUGT1, SUMO3, UBE2V1not in the datasetCreb, hemoglobin, Hsp70, Ifi47, ISGF3, IWS1, NLRP12, Nlrp4a, RNA polymerase II, Secretase gamma, Stat1-Stat2, UBE2F
Nervous System Development and Function, Organ Morphology, Cell Morphology	48	22	up-regulatedACTA2, ACTB, ACTG2, CCT3, CCT4, CLTC, DCTN1, DNM1, DPYSL2, GAP43, GNAQ, MAP2, MAP1B, MARCKSL1, NCAM1, SPTAN1, SYN1, TRRAPdown-regulatedCDK5, CYFIP2, EPB42, WASF1not in the datasetActin, Alpha Actinin, Alpha tubulin, Beta Tubulin, Calmodulin, Clathrin, F Actin, G-Actin, Hsp90, PLC gamma, Profilin, Spectrin, Tubulin
Molecular Transport, Small Molecule Biochemistry, Cell Cycle	43	21	up-regulatedAPI5, BSG (includes EG:12215), CAPN9, CECR6, GNAO1, Hmgb1 (includes EG:100041307), Hmgb1 (includes EG:25459), HSD17B4, OPCML, PNP, PSMD2, RQCD1, WDR72down-regulatedCEP290, FBXL16, GANAB, HUWE1, PCM1, PELP1, PSMC3, TANC2not in the datasetATP1B2, BCAS3, HTT, JKAMP, miR-30c-5p (and other miRNAs w/seed GUAAACA), miR-340-5p (miRNAs w/seed UAUAAAG), NDRG1, PAAF1, PPIC, PRNP, RB1, Serpina3g (includes others), TP53 (includes EG:22059), UBA5
Late vs mock
Cellular Assembly and Organization, Nervous System Development and Function, Cell Death	48	22	up-regulatedACO2 (includes EG:11429), ACTB, CAMK2A, CCT3, CCT5, CLTC, DNM1, GNAQ, HSPA8, MBP, MSN, PPP2R1A, SPTAN1, SPTBN1, STXBP1, SUMO3, SYN1, VIMdown-regulatedDPYSL2, GARS, NAPA (includes EG:108124), TCP1not in the datasetActin, Alpha Actinin, Alpha catenin, Alpha tubulin, Beta Tubulin, Calmodulin, Clathrin, Dynamin, F Actin, Hsp27, PLC gamma, Spectrin, Tubulin
Cell Death, Developmental Disorder, Neurological Disease	42	21	up-regulatedCTNNB1, ENO1, GFAP, GIT1 (includes EG:216963), HBB, HLA-C, PSMD2, PTPRZ1, SOD1, STAT1, STAT2, TAPBP, TRRAPdown-regulatedAPP, CSNK2A1, FASN, LRP1 (includes EG:16971), PELP1, PRKACB, SFPQ, SUGT1not in the dataset26s Proteasome, Akt, Cyclin A, Cyclin E, ERK1/2, Focal adhesion kinase, Histone h4, Hsp70, Hsp90, MHC Class I (complex), MHC Class II (complex), NFkB (complex), RNA polymerase II, Secretase gamma
Molecular Transport, Cellular Function and Maintenance, Nucleic Acid Metabolism	38	19	up-regulatedALB, ALDOA, API5, APOA1, ARPC5, ATP1A1, ATP1B1, ATP2B2, ATP5B, CAPN9, HEPACAM, HP, HPX, METAP2, OPCML, TF, WDR72down-regulatedCyfip2, TANC2not in the datasetAGT, APOC1, APOF, ATP5, ATP synthase, CACNA1A, calpain, CD163, CHD1L, FXYD2, HDL, hemoglobin, HTT, miR-340-5p (miRNAs w/seed UAUAAAG), miR-488-3p (and other miRNAs w/seed UGAAAGG), RBP4
Late vs Early
Cell Morphology, Cellular Assembly and Organization, Cellular Function and Maintenance	40	19	up-regulatedACTB, ARL8B, CAMK2A, CDK5, CTNNB1, CTTN, DNM1, HSPA8, TUBB, WASF1down-regulatedAPP, CRMP1, DPYSL2, DPYSL3, MAP2, MAP1B, NAPA (includes EG:108124), NCAM1, TCP1not in the dataset26s Proteasome, Actin, Beta Tubulin, Calmodulin, Alpha tubulin, CaMKII, CRMP, Dynamin, F Actin, Focal adhesion kinase, Hsp27, Hsp70, Hsp90, PLC gamma, Secretase gamma, Tubulin
Organismal Injury and Abnormalities, Respiratory Disease, Hematological Disease	38	18	up-regulatedAHSG, ALB, CAMK4, CSNK2A1, EEF2, GFAP, HBA1/HBA2, HBB, RPS21, STAT1, SUMO3, TAPBP, TF, UBE2V1, VIMdown-regulatedGARS, PRKACB, SFPQnot in the datasetAkt, APOA4, Cbp/p300, Ceacam1, Creb, DEFB103A/DEFB103B, DEFB4A/DEFB4B, ELP2, HDL, hemoglobin, Ifi47, IFIT1B, NFkB (complex), RNA polymerase II, SPINK7, Stat1 dimer, UBE2F
Infectious Disease, Endocrine System Development and Function, Energy Production	35	16	up-regulatedATP6V1B2, CAD, CBR1, CNNM3, GANAB, HSDL1, KHSRP, RANBP3, RRAGC, VPS45down-regulatedCAT, ABCF3, ACOT7, CLCN6, HSD17B4, PCM1not in the datasetACIN1, ATP6AP1, GTF2H4, HADH, HSD17B7, HSD17B10, KHK, LAMTOR1, LAMTOR2, LAMTOR3, MOCS2, NOA1, PITPNA, PTP4A2, RRAGB, SLC35E1, TMEM173, TOE1, UBC