Introduction
Materials and methods
Study cohort
Gene expression profiling
Statistical analysis
Deriving co-expressed gene modules
Motif analysis
Particles
In vitro analysis
Animal model
Flow Cytometry analysis
ELISA, quantitative real-time PCR and Western blotting
Results
Co-expressed gene modules correlated with PM exposure
City | Gender | Age (year) | |||
---|---|---|---|---|---|
Female | Male | Median | Min | Max | |
BeiJing | 15 (62.50%) | 9 (37.50%) | 29.5 | 23 | 48 |
TaiYuan | 42 (80.77%) | 10 (19.23%) | 32 | 19 | 82 |
ShiJiaZhuang | 35 (36.84%) | 60 (63.16%) | 43 | 21 | 80 |
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 |