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Table 2 Molecular network analysis using IPA

From: Different responses to oxidized low-density lipoproteins in human polarized macrophages

Top 5 Networks in M0
ID Molecules in Network Score Focus Molecules Top Functions
#1 BARX2, CD226, CRABP1, CTH, Cytokeratin, FOLR2, FOS, GCLM, GCNT1, HHEX, HTATIP2, IGDCC3, KCNJ2, KRT8, KRT18, KRT20, KRT6A, LPCAT3, MAF, MAFB, MAFF, MAFG, MT1A, musculoaponeurotic fibrosarcoma oncogene, NFE2L3, NRF1, PAX6, PLAGL1, PVR, S100P, TGFBI, TH1 Cytokine, TLE1, TMSB4, TMSB4X 33 31 Cellular Assembly and Organization,
Cellular Function and Maintenance,
Hair and Skin Development and Function
#2 Alpha tubulin, APEX2, ARRDC3, CALB2, Calbindin, CSF1, CXORF21, DHCR24, DUB, EHMT2, FAM105A, FAM107A, GSC, HDAC6, HOOK2, LMO2, LRRC58, MIR124, NTRK3, oxidoreductase, POU5F1, PPP1R12C, REST, RYK, STAU1, TRPM2, TSPAN14, Tubulin, USP12, USP28, USP34, USP41, USP48, USP49, ZBED3 28 29 Auditory and Vestibular System Development and Function,
Genetic Disorder,
Metabolic Disease
#3 ANAPC1, ANAPC2, ANAPC5, APC, ASNS, BIRC3, CD3EAP, CDC20, CHD2, CKAP2, Cpt, CPT2, Cyclin A, DTYMK, E3 RING, EIF5, GLCE, GPC1, HEXIM1, HGF, IMPDH2, Integrin alpha V beta 3, ISG20, JMJD1C, MYL12A, NAMPT, POLR1A, SLC40A1, SPATC1, SPDEF, TMEM158, TOPBP1, UBR2, Vegf, VHL 28 29 Protein Degradation, Protein Synthesis,
Cardiovascular System Development and Function
#4 ALDH2, ASXL1, C14ORF1, CBX4, CCDC106, CDK5RAP2, Cyclooxygenase, DIO3, DUSP8, FHL1, JDP2, LSM2, MIP1, MYBPC3, P38 MAPK, PCGF2, PHYHIP, PLEKHN1, PORCN, SEMA7A, SENP2, Stat1 dimer, STK36, SUFU, Tnf receptor, TNFRSF9, TNFRSF11A, TNFSF9, TRAF, TRAF1, TRAF5, TRAF2-TRAF5, TRAIP, TREM1, WNT4 27 28 Cellular Assembly and Organization,
Cellular Function and Maintenance,
Skeletal and Muscular System Development and Function
#5 ANKRD29, APEX1, BAG5, CKB, CKMT1B, CNOT3, CNOT6, CNOT8, Creatine Kinase, DNAJA4, DNAJB6, DNAJC15, DNMBP, Fibrinogen, Hsp70, Hsp90, Hsp22/Hsp40/Hsp90, HSPA2, HSPA1A, ICAM1, IFT52, IP6K2, MIR1, Nos, Pka catalytic subunit, PLSCR1, SH3KBP1, SLC25A30, SPRY2, SRXN1, TIMP3, TNKS1BP1, TNPO2, TRIM2, XPNPEP3 26 27 Cellular Assembly and Organization,
Cellular Development,
Cellular Growth and Proliferation
Top 5 Networks in M1
ID Molecules in Network Score Focus Molecules Top Functions
#1 ABCD1, AQP8, C13ORF15, CALML4, CCNE2, CDC7, DBF4, FXYD6, GALM, GIN1, GYG1, GYG2, GYS1, H1FX, HNMT, HYAL2, LPCAT3, ORC2L, ORC5L, ORC6L, OVOL1, PDLIM5, PHGDH, PSPH, RBM19, RBMS3, SBNO2, SEMA7A, SLC23A2, SLC25A14, SLC35A1, TBC1D1, TGFB1, TRIM7, UGDH 41 35 Carbohydrate Metabolism,
DNA Replication, Recombination, and Repair,
Embryonic Development
#2 ATAD3B, CAPZB, CHTF18, CPD, CPT2, FXC1, FXYD1, GAMT, GPC1, GTF3C2, GTF3C4, HMG CoA synthase, HMGCS1, HNRNPA0, IQGAP3, IREB2, LMNB2, LSM2, LSM6, LSM7, MINA, Mir125b (mouse), MYC, Ndpk, NME2, NME6, NME7, PDS5B, RAD21, RANBP6, REC8, RFX2, RNGTT, RRM2B, TOR2A 34 32 Cellular Assembly and Organization,
Genetic Disorder,
Metabolic Disease
#3 ACTN4, APEX2, ATRX, DNA-directed DNA polymerase, Erm, HOOK2, ICAM1, IGSF8, LAS1L, LIG3, LIG4, LRSAM1, MARCH3, MYOZ1, NEIL1, NOM1, PNKP, POLE2, POLG2, POLM, RNF2, RNF6, RNF10, RNF25, RNF166, RNF185, SLC9A1, TRIM37, TRP, TRPC4, UBE2D2, UBE2E3, UBE2 H (includes EG:7328), VIL1, ZNRF1 34 32 DNA Replication, Recombination, and Repair,
Gene Expression,
Cell-mediated Immune Response
#4 ARL15, BRD1, BTBD2, C14ORF1, C1ORF103, CCDC106, CCDC90B, CD3EAP, CDKN3, DNA-directed RNA polymerase, EGLN1, EHMT2, FEZ1, FXR1, GTF3A, histone-lysine N-methyltransferase, KBTBD7, KIF11, KIF2C, KLK10, LMO2, MELK, POLR1A, POLR3 D, POLR3E, POLR3F, RIT1, SETDB1, S TAB2, THAP8 (includes EG:199745), TLE1, TMSB4X, UNC119, Vegf, ZNF24 (includes EG:7572) 30 32 Cell Cycle,
Cellular Assembly and Organization,
DNA Replication, Recombination, and Repair
#5 ABCC1, ABCD3, ACIN1, ATP5B, ATPase, CRISPLD2 (includes EG:83716), DTX1, DUSP1, E2F1, FABP1, FAM177A1, GRAP, IL34, Immunoglobulin, INHBA, INHBC, LIF, MAFF, MARK4, MIR124, MYH9, NAA15, NOTCH1, POMC, RDH10, RSF1, RYK, SKIV2L, SLC22A18AS, S TAB1, SYNGR2, Trypsin, WRN (includes EG:7486), WWP1, ZNF790 30 31 Cellular Development,
Nervous System Development and Function,
Hematological System Development and Function
Top 5 Networks in M2
ID Molecules in Network Score Focus Molecules Top Functions
#1 AKR1C3, ARL15, C1ORF103, CETN3, DCP1A, DCTPP1, DDX6, DDX20, DNA-directed RNA polymerase, DUB, ETV3, FILIP1L, FXYD6, GANAB, GSTM3 (includes EG:2947), GTF3C4, GXYLT1, JMJD1C, NUP155, POLR1A, POLR1E, POLR3F, PRMT1, RHOF, RIF1, SDCCAG8, SNRPA1, TARS, TRAF6, UNC119, USP20, USP41, USP45, VHL, ZFP161 36 33 Infection Mechanism,
Infectious Disease,
Cell Cycle
#2 ATN1, BANP, C8ORF4, CBFA2T2, CLK2, CLOCK, CRY1, DBP, EIF2B1, Fascin, H1FX, HIST1H2AE (includes EG:3012), Histone H1, HNRNPL, Importin beta, KHDRBS3, KIAA0913, LBR, LTBP4, LTC4 S, MAST2, OGG1, Pkc(s), RNF19A, SAFB, SDCBP2, SLC20A2, SRPK1, STK36, SUFU, TIMELESS, TM4SF1, TPM2, XPC, ZNF652 32 31 Behavior,
Nervous System Development and Function,
Lipid Metabolism
#3 ATF7IP, ATPase, BACE1, CAPN3, CASP2, CASP7, CASP10, Caspase, CTRL, ENTPD2, hydrolase, ICAM1, IDE, ITM2C, KIAA1632, KYNU, LGMN, MAGED1, MEOX2, NAIP, NANP, NGFR, NUP160, PAPPA, peptidase, PLEKHF2 (includes EG:79666), RECQL5, RTN3, SENP5 (includes EG:205564), SPPL2B, SPTBN1, THTPA, UBAC2, UBR5, XAF1 32 31 Protein Degradation,
Protein Synthesis,
Post-Translational Modification
#4 API5, ARRDC3, ASPH, Calbindin, CKB, CNNM4, COX11, COX15, COX10 (includes EG:1352), CPT1B, Creatine Kinase, Cytochrome c oxidase, ENO3, FICD, FOXP1, GPRASP2, HTR2B, HTT, JAKMIP1, KLF16, NDUFS1, NEFH, PHB (includes EG:5245), PPP1R16B, RCOR2, REST, RGS14, RNF34, SASH1, SCN4B, SNN, STRN, Thymidine Kinase, VAPA, WAC 32 31 Gene Expression,
Neurological Disease,
Cellular Compromise
#5 ALDH7A1, BPI, Cbp, Ciap, CLIP2, CST7, DBT, DUSP2, G0S2, GFPT2, KLF3, KRT19, lymphotoxin-alpha1-beta2, MICA, NFkB (complex), NKIRAS1, PELI3, POU2F2, RBCK1, REL/RELA/RELB, RNF216, S100P, S100Z, SH3RF1, SIAH2, SLC2A6, SNIP1, SUMO4, TNIP2, TRIM32, TRIM69, TXNRD1, WTAP, ZMYND11, ZNF71 30 30 Carbohydrate Metabolism,
Lipid Metabolism,
Small Molecule Biochemistry
  1. Molecular network analysis was performed using IPA software. The top 5 groups of molecules in the network are listed in order of network score, which IPA calculates as shown below. We focused on the highest scoring network #1 in M1 macrophages, which had a score of 41 and included 35 molecules matched with the Ingenuity Knowledge Base.
  2. Network Score = -log10(P-value)