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Table 3 Top affected gene-gene interaction networks after sub-chronic SWCNT exposure in transformed BEAS-2B cells

From: Gene expression profile of human lung epithelial cells chronically exposed to single-walled carbon nanotubes

Top diseases and functions

Molecules in network a,b

Score

Focus molecules c

Cellular growth and proliferation, hematological system development and function, humoral immune response

ADAM15, ADRBK2, ATP5B, BCL10, BCR (complex), CHGA, CR2, CRHR1, ERK1/2, FGR, GNAZ, HOPX, HSD11B2, HSPD1, HTATIP2, IgG1, Igg3, IgG2b, IGLL1/IGLL5, Igm, insulin, ITCH, Jnk, MFGE8, NEU1, PAK2, PAX4, PPP1R1B, Ras, RASGRP1, SH2B2, SH2D2A, TAS1R1, Vegf, ZNF24

35

25

Connective tissue disorders, inflammatory disease, skeletal and muscular disorders

C1R, CD33, CD59, CDON, G6PD, HLA-A, HLA-B, HLA-C, HLA-E, Ifnar, IgG, IKK (complex), immunoglobulin, interferon alpha, KIR, KRT31, MYO1E, NFAT5, NFkB (complex), P38 MAPK, PI3K (family), PIM1, Pkc(s), RHOB, RNF34, RTKN, SCARB1, SIRPA, SLC6A6, Tap, TAPBP, TNFSF10, TRAF3IP2, USP11, USP18

33

24

Cell death and survival, embryonic development, organismal development

ADAM17, AFF4, AKT2, Akt, AMPK, Ap1, BHLHE40, CD68, CELF1, CSNK1E, CSNK1G2, Cyclin A, DVL1, estrogen receptor, F actin, FMR1, GSK3B, HMGB3, HMGN5, Hsp70, IGFBP2, LCP1, LDL, MGLL, MUC4, OSGIN1, PDGF BB, PI3K (complex), PMAIP1, Ppp2c, PURA, SF3B3, STRN, USP6, USP33

33

24

Cellular compromise, skeletal and muscular system development and function, post-translational modification

ARHGEF9, ATP13A2, CD3, Cg, Creb, CTSB, DUSP9, ERK, FBN1, FGF3, FSHR, GSTM4, Hdac, Histone h3, Histone h4, HSD17B1, IFI44, IFI44L, IgG2a, KDM3A, Lh, MCOLN1, MT1F, MT1X, NDRG1, NDRG4, NES, NPNT, ORAI1, OXT, PGK1, SOX12, STAT5a/b, STK17A, TCR

33

24

Cell morphology, cellular assembly and organization, cellular development

ACBD7, ADAM22, ANK1, AR, AS3MT, ATP5S, ATP6V0E2, ATP8B1, CACNA1E, CDC6, CHD8, DLG4, FARP1, GLUL, GPR182, GSTM1, HILPDA, HIST1H1A, IGF1R, KCNA4, KCNAB2, MCM8, NIPSNAP1, NUPR1, PPT2, RAB18, RCN2, SIPA1L1, SOX11, ST6GALNAC6, SYNGAP1, TEX2, TMEM30A, WNK1, ZSCAN16

21

18

Respiratory system development and function, tissue morphology, cell cycle

26 s Proteasome, ACTC1, ACTN1, ACTR2, ACTR3, BNIP3L, CAP2, CARD10, CKAP2, EBAG9, ELMOD3, ENC1, FAM89B, FSH, GEM, IGLL1/IGLL5, ING2, JMJD6, MED26, MT1L, NOL3, NR3C1, PRPH, PSMB1, RAB11A, RDM1, RNA polymerase II, SCAF8, SERTAD2, SFTPC, SIAH2, SMARCC1, TFDP2, TUBA4A, USP13

16

15

Cancer, gastrointestinal disease, hepatic system disease

ACOT11, AHCY, ANXA7, ARL6IP1, ARNT, ASS1, AXIN1, AXIN2, BCLAF1, CAMLG, CCDC80, CYP1A1, EPHX1, FAM120A, FBXW7, HIST1H1C, IGFBP2, KAT5, KITLG, KREMEN2, MED13L, MT1H, N-cor, NCOR2, NQO1, PIAS2, PSMF1, PTGDS, PTP4A3, RBBP4, SERPINB6, SIDT2, STOX1, TCF7L2, TP53

16

15

Cell morphology, cell-to-cell signaling and interaction, nervous system development and function

AIG1, ALDH3B1, C11orf30, CABYR, CACNA2D1, CHMP4B, COX10, CYFIP2, DGKZ, DMD, DNAJB6, DTNB, DYRK1A, HDAC4, HYOU1, INS, LEPR, Map4k4, MARK3, OPN4, Pdx1, PFKM, PPFIA1, proinsulin, SNCA, SNTB2, SPARC, SPOP, TNRC6B, TRIM44, TUBB4A, VEGFA, VGF, YWHAG, YWHAH

16

15

DNA replication, recombination, and repair, cellular compromise, cell death and survival

ATP6V0E1, BAG1, BAX, BGN, BRCA1, BRCA2, CCND1, CEL, CKB, DDX5, DNAJA1, DPYSL3, FANCD2, GATA1, GFI1B, GSK3A, H3F3A/H3F3B, Hbb-b2, HSPA4, HSPD1, LATS1, LINC00467, MAPT, NGFR, NME4, OPA1, ROCK2, SFN, SPOCK2, STIP1, TLE1, UBE2N, USP11, ZFPM1, ZNF324

15

14

Lipid metabolism, molecular transport, small molecule biochemistry

AP1M2, APOA1, APOC1, ARCN1, CBS, CCL1, CCL22, CETP, CLIC4, COG3, COPG1, COPZ1, CXCL5, ERN1, EYA4, GSTA1, HLA-J, HYOU1, IFNB1, LCAT, MGLL, NPEPPS, Pdx1, PEX6, PHLDB2, PPARG, PTGES2, RGS14, RNASE1, TBXAS1, TMEM173, TNF, TPM2, Trim30a/Trim30d, XBP1

15

14

  1. aThe network was based on SWCNT vs. control comparison, p < 0.05 and fold changes >2.
  2. bCapitalized names indicate genes while lower case names indicate complexes.
  3. cThe number of differentially expressed genes in each network are reported.

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