Twenty-three generalised biological process annotations analysed by gene set linkage analysis in peripheral blood mononuclear cells
| Generalised biological process | Type of gene set* | Up/down | GO/PID term | p Value† | Overlapping gene(s)‡ |
|---|---|---|---|---|---|
| TLR signalling and TLR-like receptor signalling | C-DE, D3:D0 | Up | PID:200209 | ≤1e-5 | S100A8, S100A9, TLR4 |
| T-DcoE, D0-7:D0-3 | N/A | GO:0034138, GO:0002224, GO:0034134, GO:0002756, GO:0034130, GO:0034142, GO:0002755, GO:0008063 | ≤1e-5 | MAP2K1, ATF1, JUN | |
| C-DcoE, D0-3:D0-7 | N/A | GO:0034130, GO:0008063 | ≤1e-5 | MAP3K1 | |
| TGF-beta receptor signalling | C-DE, D3:D0 | Down | PID:200228 | ≤1e-5 | TGFBR2 |
| Regulation of SMAD protein and SMAD2/3 signalling | T-DcoE, D0-7:D0-3 | N/A | GO:0010862 | ≤1e-5 | CEBPB, VDR, CNNM371, JUN |
| ALK1 signalling | C-DE, D3:D0 | Down | PID:200149 | ≤1e-5 | TGFBR2 |
| IFN-gamma mediated signalling and IFN-gamma pathway | C-DE, D3:D0 | Down | GO:0060333, GO:0032729 | ≤1e-5 | – |
| C-DcoE, D0-3:D0-7 | N/A | PID:200130 | ≤1e-5 | STAT1 | |
| Notch receptor and Notch signalling | C-DE, D3:D0 | Up | GO:0007219 | ≤1e-5 | NRG1 |
| T-DE, D7:D0 | Down | GO:0007220 | ≤1e-5 | – | |
| T-DcoE, D0-7:D0-3 | N/A | PID:200015 | ≤1e-5 | NOTCH3 | |
| Regulation of IL-6 biosynthetic process | C-DE, D3:D0 | Up | GO:0045410 | ≤1e-5 | – |
| Response to IL-1 | C-DE, D3:D0 | Up | GO:0071347 | ≤1e-5 | LCN2 |
| Regulation of IL-2 biosynthetic process and IL-2 signalling | C-DE, D3:D0 | Down | PID:200185, GO:0045086 | ≤1e-5 | LCK |
| IL-4-mediated signalling events | C-DE, D3:D0 | Down | PID:200022 | ≤1e-5 | – |
| IL-5-mediated signalling events | C-DE, D3:D0 | Down | PID:200107 | ≤1e-5 | – |
| IL-12 signalling and IL-12-mediated signalling events | C-DE, D3:D0 | Down | PID:200045, PID:200230 | ≤1e-5 | GZMA, LCK |
| IL-23-mediated signalling events | C-DE, D3:D0 | Down | PID:200155 | ≤1e-5 | – |
| CXCR4-mediated signalling events | C-DE, D3:D0 | Down | PID:200099 | ≤1e-5 | LCK |
| SHP2 signalling | C-DE, D3:D0 | Down | PID:200083 | ≤1e-5 | LCK |
| c-Kit-mediated signalling events | T-DcoE, D0-7:D0-3 | N/A | PID:200182 | ≤1e-5 | SH2B3 |
| C-DE, D3:D0 | Down | PID:200182 | ≤1e-5 | – | |
| TNF receptor signalling | T-DE, D7:D0 | Down | PID:200102 | ≤1e-5 | TNFAIP3 |
| Cellular response to TNF | T-DE, D7:D0 | Up | GO:0071356 | ≤1e-5 | LCN2 |
| HIV-1 Nef: negative effector of Fas and TNF-alpha | C-DcoE, D0-3:D0-7 | N/A | PID:200156 | ≤1e-5 | – |
| C-DE, D3:D0 | Down | PID:200156 | ≤1e-5 | FAS, CASP2 | |
| Alpha-synuclein signalling | C-DE, D3:D0 | Down | PID:200220 | ≤1e-5 | – |
| Syndecan-1-mediated signalling events | C-DE, D3:D0 | Down | PID:200157 | ≤1e-5 | – |
| Plexin-D1 signalling | C-DE, D3:D0 | Up | PID:200122 | ≤1e-5 | ITGB1, NRP1, ITGA1, ITGAV |
| ErbB signalling | T-DcoE, D0-7:D0-3 | N/A | PID:200134 | ≤1e-5 | ATF1, JUN, BAD, MAP2K1, RALGDS |
| C-DE, D3:D0 | Down | PID:200205, PID:200011 | ≤1e-5 | LCK |
*Type of gene set. C-DE, D3:D0, genes differentially expressed between days 0 and 3 in the control (C) group; T-DE, D7:D0, genes differentially expressed between days 0 and 7 in the transplantation (T) group; T-DcoE, D0-7:D0-3, differentially co-expressed gene clusters, with co-expression in the transplantation (T) group (days 0 and 7) but not in the control (C) group (days 0 and 3); C-DcoE, D0-3:D0-7, differentially co-expressed gene clusters, with co-expression in the C group (days 0 and 3) but not in the T group (days 0 and 7). N/A, not applicable.
†The p value reflects the reliability/robustness/biological significance of the identified functional interaction.
‡Overlapping genes are those that have been annotated to the biological process.
GO/PID, gene ontology/pathway interaction database; IFN, interferon; IL, interleukin; TGF-beta, transforming growth factor-beta; TLR, toll-like receptor; TNF, tumour necrosis factor.