Table 1.
List of predicted signaling pathways for differentially expressed genes between the sham and normal groups
| Pathway | Count | % | p | Corrected pa | FE | Genes |
|---|---|---|---|---|---|---|
| Systemic lupus erythematosus | 17 | 2.55 | 5.51E-06 | 7.82E-04 | 3.85 | Tnf, C6, Hist1h2ail, LOC498276, Hist2h3c2, RT1-DMa, C1r, C1s, Cd40, RT1-DMb, C1qc, C1qa, C1qb, Fcgr2b, Hist2h2ac, Fcgr1a, Fcgr2a, C2, Fcgr3a |
| Toll-like receptor signaling pathway | 15 | 2.25 | 9.99E-05 | 7.07E-03 | 3.40 | Ccl3, Tnf, Ly96, Tlr2, Tlr4, Mapk11, Cd40, Tlr6, Cxcl10, Fos, Myd88, Irf5, Map3k8, Cd14, Spp1 |
| Complement and coagulation cascades | 13 | 1.95 | 1.21E-04 | 5.71E-03 | 3.79 | A2m, C5ar1, C6, C1r, Serping1, C1s, C1qc, C1qa, Vwf, C1qb, Cfh, C2, Cfd |
| Natural killer cell mediated cytotoxicity | 15 | 2.25 | 3.14E-04 | 1.11E-02 | 3.06 | Icam1, Ptpn6, Tnf, Itgb2, Hcst, Rac2, Fcgr2b, Plgc2, Fcer1g, Shc1, Fcgr2a, Fcgr3a, Ifngr1, Tyrobp, Lcp2, Syk |
| Cell cycle | 17 | 2.55 | 3.73E-04 | 1.05E-02 | 2.75 | LOC298795, Ttk, Pkmyt1, Cdk6, Chek1, Cdc20, Sfn, Mcm2, Pttg1, Mcm3, Mcm4, Tgfb1, Mcm6, Ccnd1, Plk1, Bub1, Ccna2, Myc |
| MAPK signaling pathway | 27 | 4.05 | 4.88E-04 | 1.15E-02 | 2.07 | Tnf, Hspa1b, Nfkb2, Tgfb1, Map3k6, Tnfrsf1a, Fos, Bdnf, Rac2, Rasgrp1, Rasgrp2, Map3k8, Rras, Myc, Fgf2, Ptpn7, Tgfbr2, Nr4a1, Cacng3, Mapk11, Flna, Dusp5, Pla2g4a, Dusp1, Ntrk1, Hspb1, Cd14 |
| Focal adhesion | 21 | 3.15 | 1.22E-03 | 2.44E-02 | 2.20 | Parvg, Tln1, Col4a1, Col3a1, Igf1, Itga4, Birc3, Flna, Pak6, Vwf, Ccnd1, Rac2, Vegfa, Col6a2, Rhoc, Shc1, Lamc1, Col11a2, Parva, Spp1, Fn1 |
| Hematopoietic cell lineage | 12 | 1.80 | 1.29E-03 | 2.27E-02 | 3.14 | Sept5, Tnf, Cd44, Cd8b, Fcgr1a, Il4ra, Anpep, Itga4, Cd1d1, Cd14, Csf2ra, Csf1r |
| Chemokine signaling pathway | 19 | 2.85 | 1.58E-03 | 2.47E-02 | 2.27 | Adcy4, Ccl3, Fgr, Ncf1, Hck, Ccl9, Pf4, Cx3cl1, Stat3, Ccl6, Cxcl10, Ccr5, Rac2, Cxcr4, Cxcl16, Rasgrp2, Rhoc, Shc1, Jak3 |
| ECM-receptor interaction | 12 | 1.80 | 1.77E-03 | 2.48E-02 | 3.02 | Sept5, Vwf, Sdc1, Col4a1, Cd44, Col3a1, Col6a2, Lamc1, Itga4, Col11a2, Fn1, Spp1 |
| Cytokine-cytokine receptor interaction | 20 | 3.00 | 3.26E-03 | 4.13E-02 | 2.07 | Ccl3, Tnf, Tnfrsf12a, Il18, Il4ra, Tgfbr2, Pf4, Cd40, Cx3cl1, Cxcl10, Tnfrsf1a, Tnfrsf1b, Ccr5, Cxcr4, Il10rb, Cxcl16, Il13ra1, Csf2ra, Ifngr1, Csf1r |
| Leukocyte transendothelial migration | 14 | 2.10 | 3.75E-03 | 4.35E-02 | 2.48 | Icam1, Ncf1, Ncf4, Sipa1, Mapk11, Itgb2, Itga4, Cldn14, Cyba, Rac2, Cxcr4, Plcg2, Rhoc, Msn |
| Lysosome | 14 | 2.10 | 4.36E-03 | 4.66E-02 | 2.44 | Tcirg1, Ctsz, Gusb, Lgmn, Napsa, Cd63, Ctsl1, Slc11a1, Ctsk, Cd68, Laptm5, Ctsd, Ctsc, Cln5 |
a
p-value after Benjamini-Hochberg correction
The full names of genes are described in Supplementary Table S1.
The genes italicized denote downregulated genes in the sham group compared to the normal group.
ECM, extracellular matrix; FE, fold enrichment; MAPK, mitogen-activated protein kinase