Table 2.
GO biological processes from differentially expressed genes between biopsies A and B in the glomerular compartment
| GO biological process | Ref. list | Hits | Fold enrichment | Biopsy A versus B | P |
|---|---|---|---|---|---|
| Complement activation, alternative pathway (C3, C7, CFH) | 13 | 3 | >100 | >B | 1.97 ×10−02 |
| IFNγ-mediated signaling pathway (HLA-A, HLA-DRB1, PML, VCAM1, PRKCD, STAT1, IRF3, IRF7, HLA-DRB3) | 71 | 9 | 66.6 | >A | 1.23 × 10−10 |
| Type I IFN signaling pathway (HLA-A, STAT1, IRF3, PML, MX1, IRF7) | 65 | 6 | 48.5 | >A | 1.42 × 10−02 |
| Negative regulation of leukocyte apoptotic process (CCL19, LILRB1, BCL6, IRF7) | 44 | 4 | 47.7 | >B | 1.42 × 10−03 |
| Regulation of immunoglobulin-mediated immune response (C3, LTA, CD40, BCL6) | 48 | 4 | 43.8 | >B | 2.00 × 10−02 |
| Regulation of IL12 production (RELA, CCL19, LILRB1, CD40) | 51 | 4 | 41.2 | >B | 2.54 × 10−02 |
| T cell co-stimulation (CCL19, HLA-DRB1, DPP4, ICOS, HLA-DRB3) | 82 | 5 | 32.0 | >A | 4.56 × 10−03 |
| PRR signaling pathway (RELA, MAPKAPK2, IRF3, IRF7, S100A8) | 122 | 5 | 21.5 | >A | 3.14 × 10−02 |
| Regulation of humoral immune response (C3, CFH, LTA, C1QB, C7) | 128 | 5 | 20.5 | >B | 3.96 × 10−02 |
| Positive regulation of IκB kinase/NF-κB signaling (RELA, CCL19, LITAF, CD40, HLA-DRB1, TRAF5, IRF3) | 183 | 7 | 20.1 | >B | 4.73 × 10−04 |
Ref. list (reference list) indicates the number of genes in a particular biological pathway. Hits, indicates the number of differentially expressed genes included in the pathway. Fold enrichment represents the enrichment score that reflects the degree to which a set of differentially expressed genes is overrepresented in the biopsies A or B [18]. The P-value is the estimation of significance level of the enrichment score.
PRR, pattern recognition receptor.