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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)