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Table 2 Transcription factors (TF) underlying the co-expressed gene modules correlated with PM exposure (“cyan”, “brown”, “blue” and “turquoise”). TFs of which the binding motifs are significantly overrepresented in the co-expressed gene modules (FDR < 0.1); or the target genes are overrepresented in the eigen genes of each module (q-value < 0.05) are listed along with the KEGG pathways enriched (FDR < 0.05) in each module

From: IRF4 and STAT3 activities are associated with the imbalanced differentiation of T-cells in responses to inhalable particulate matters

Co-expressed Modules Binding motifs enriched in upregulated genes Transcription factor activities KEGG Pathway enrichment
cyan Nrf2(bZIP); NFkB-p65(RHD); n-Myc (bHLH); PIF4(bHLH); RAR:RXR (NR); IRF (bZIP,IRF)/Th17-BatF NFKB1, RELA, JUN, NFIC, CEBPB, REL, CEBPD, SP1, CTNNB1, CDX1, STAT1, DLX1, STAT6, RELB, STAT3, DLX2, CEBPG, BCL6, PDX1, TFAP2A, STAT2, GATA4, JUNB, GATA1, JUND, CREB1, YY1, FOS, LEF1 Viral protein interaction with cytokine and cytokine receptor; IL-17 signaling pathway; Chemokine signaling pathway; Cytokine-cytokine receptor interaction; Salmonella infection; Rheumatoid arthritis; TNF signaling pathway; Fluid shear stress and atherosclerosis; Tuberculosis; NF-kappa B signaling pathway; AGE-RAGE signaling pathway in diabetic complications
brown HOXA2(Homeobox); Hoxb4(Homeobox); STAT4(Stat);Pax7(Paired,Homeobox); E2A(bHLH); Stat3(Stat); STAT6(Stat) MYC, SP1, TP53, STAT1, CEBPA, STAT3, HOXD3 PD-L1 expression and PD-1 checkpoint pathway in cancer
blue FOXP1(Forkhead); Fli1(ETS); GABPA (ETS); GATA3(Zf);RUNX-AML (Runt); E2A(bHLH); ox2(HMG); ETS1(ETS); Eomes(T-box) MYC, TFAP2A, SP1, ETS1, SPI1, GLI2, USF1, SP2, RELA, SP3, ELK1, POU2F2, REL, STAT3, POU1F1, ETV4, RELB, FOXO3, NFKB1, USF2, RUNX1, FOXO1, E2F1, CTNNB1, MYB, E2F6, MYBL2, RARA, GLI1, PPARD, JUN, RARG, PAX6, NFYA, TP53 Viral protein interaction with cytokine and cytokine receptor; ErbB signaling pathway; Epithelial cell signaling in Helicobacter pylori infection
turquoise Fli1(ETS), ETS1(ETS); ELF1(ETS); Etv2(ETS); EABPA (ETS); Ets1-distal (ETS); RUNX (ETS,Runt) CREB1, RBPJ, SP1, MYC, ATF1, CREBBP, SPI1, NFKB1, RELA, SREBF2, SREBF1, TP53, ETV4, E2F1, EGR1, FOXO1, NOTCH1, TFAP2A, YY1, BRCA1, BCL3, ETS1, TCF7L2, USF2, ATF6, JUN, STAT3, ESR1, CREM, PPARA, SMAD1, E2F6, FOXO3, PPARG, WT1, NFATC2, FLI1, RFX1, EGR4, OLIG1, FOXP1, CEBPB, PPARD, CTNNB1, ELK1, STAT5B, IRF9, STAT5A, ATF2, NFYA, GLI2, AR, USF1, STAT1, RELB, ID1, MYBL1, POU2F2, SMAD3, SMAD2, E2F4, ERG, FOXH1, CEBPA, REL, NFIC, ARNT, FEV, POU1F1, SP3, HOXA5, CEBPE, RARB, FOXO4, MYB, NFIA, NFATC1, SOX10, RARA, NR2F2, MITF, GABPA, HBP1, RARG, STAT2, SMAD4, HIF1A, NR1H2, NR1H3, TCF7, RUNX2, ATF4, NFE2L2, TBP, HNF4A, JUNB, NR2F1, CEBPD, GLI1, GATA1 Lysine degradation; RNA degradation; N-Glycan biosynthesis; Ubiquitin mediated proteolysis; Valine, leucine and isoleucine degradation; Spliceosome; RNA transport; Hepatitis C; Propanoate metabolism; Cytosolic DNA-sensing pathway