Table IX.
The top 25 biological pathways and processes that are highly enriched in WT compared to Nrf2 null neutrophils during S. pneumoniae pneumonia
| Category | Gene sets that are enriched in WT compared to Nrf2 null neutrophils during SP pneumonia |
Genes in common that contributed to core enrichment |
|---|---|---|
| Angiogenesis and vascular development |
GO:0001568 (Blood vessel development) GO:0001944 (vasculature development) GO:0048514 (blood vessel morphogenesis) GO:0001525 (angiogenesis) GO:0060976 (coronary vasculature development) GO:0072359 (circulatory system development) GO:0072358 (cardiovascular system development) |
Fgfr2, Gata4, Fgf1,
Vegfb, Pdgfrb, Ace, Rxra, Gata6, Nrp1, Fgf2, Fgfr1, Robo1, Shh, Angpt1 |
| Noncoding RNA processes | GO:0034470 (ncRNA processing) GO:0042254 (ribosome biogenesis) GO:0034660 (ncRNA metabolic process) GO:0006399 (tRNA metabolic process) GO:0016072 (rRNA metabolic process) GO:0006364 (rRNA processing) |
Exosc3, Fdxacb1,
Exosc8, Pop5, Exosc9, Exosc7, Exosc2, Fbl |
| Glutathione (sulphur) metabolism | GO:0006790 (sulfur compound metabolic process) GO:0006749 (glutathione metabolic process) |
Gstt1, Gstm7,
Oplah, Ggt1, Idh1, Gstz1, Glo1, Gstk1, Gstp1, Gstm5, Txnrd3, Gstp2, Gsto1, Gclc, Gss, Gpx3, Cth, Gstm1, Gstm4, Gsta1, Gclm |
| Extracellular matrix structure and organization |
GO:0030198 (extracellular matrix organization) GO:0043062 (extracellular structure organization) |
Nid1, Apbb2, Egfl6,
Sulf1, Vtn, Dpp4, Prdx4, Aplp1, Foxf1, Dag1, Smoc2, Adamtsl4, Ddr1, Hspg2, Tnxb, Hpse2, Ptk2, Emilin1, Creb3l1, Fscn1, Has1, Apbb1, Pxdn, Csgalnact1, Col4a1, Lamb2, Serpinh1, Col18a1, Fgfr4, Ctgf, Ecm2, Reck, Lamc1, Mfap5, Thsd4, Foxf2, Col1a1, Olfml2a, Spock2, Eln, Myh11, Mfap4, Abi3bp, Col5a1, Wt1, Ndnf, Dpt, Ramp2, Cyr61, Col3a1, Fbln5, Tgfb2, Col5a2, Lox, Sfrp2, Cyp1b1, Ddr2, Adamts2, Gpm6b, Flrt2, Adamtsl2, Npnt, Col1a2, Itga8, Pdgfra, Egflam, Sema5a |
| Epithelial development | GO:0030324 (lung development) GO:0030323 (respiratory tube development) GO:0060541 (respiratory system development) GO:0002009 (morphogenesis of an epithelium) GO:0001655 (urogenital system development) |
Fgfr2, Fgf1, Dlg5,
Foxa1, Eya1, Wnt7b, Lama5, Wnt5a, Gli2, Foxf1, Bmp4, Spry1, Tnc, Fgf2, Igf1, Fgfr1, Gpc3, Gli3, Shh, Aldh1a2, Tcf21 |
| Cell migration and movement |
GO:0051270 (regulation of cellular component movement) GO:0090287 (regulation of cellular response to growth factor stimulus) GO:0030334 (regulation of cell migration) |
Mmrn2, Wnt5a,
Sfrp1, Itga3, Nbl1, Vegfc, Cxcl13, Bmp4, Nkx2-1, Fgf2, Tek, Tgfbr3, Fgf18, Cyr61, Sfrp2, Slit2, Bmper, Ccbe1, Angpt1 |
Gene sets were obtained from publicly available databases and GSEA was used to identify the top 25 significantly enriched gene sets (FDR< 1.97×10−5), which were subsequently sorted into related functional categories, and the genes in common that contributed to core enrichment were identified. Genes are ranked by increasing difference between mean expression levels in WT and Nrf2 deficient neutrophils, scaled by the standard deviation.