Table 3 Consistently perturbed gene sets
Gene set | | A∩ C| | | A∖ C| | | C∖ A| | |A′∩C′| | | n| |
|---|---|---|---|---|---|
        Up-regulated | |||||
Adaptive immune response (MsigDB) | 1 | 4 | 4 | 15 | 24 |
Dissolution of fibrin clot (NCI) | 2 | 1 | 2 | 3 | 8 |
Granulocytes pathway (BIOCARTA) | 3 | 0 | 1 | 10 | 14 |
Inactivation of MAPK activity (MsigDB) | 3 | 1 | 1 | 9 | 14 |
Viral genome replication (MsigDB) | 3 | 2 | 2 | 14 | 21 |
Hedgehog pathway up (NETPATH) | 3 | 2 | 1 | 16 | 22 |
Positive regulation of immune response (MsigDB) | 3 | 3 | 2 | 21 | 29 |
CD28 dependent PI3K AKT signaling (REACTOME) | 4 | 2 | 3 | 10 | 19 |
Peptidyl tyrosine phosphorylation (MsigDB) | 4 | 5 | 6 | 12 | 27 |
CDMAC pathway (BIOCARTA) | 5 | 2 | 3 | 6 | 16 |
CARDIACEGF pathway (BIOCARTA) | 5 | 3 | 3 | 7 | 18 |
CHUK NFKB2 REL IKBKG SPAG9 NFKB1 NFKBIE COPB2 TNIP1 NFKBIA RELA TNIP2 complex (CORUM) | 6 | 1 | 2 | 3 | 12 |
CD40 pathway (BIOCARTA) | 7 | 1 | 1 | 6 | 15 |
EGFR1 pathway down (NETPATH) | 8 | 13 | 13 | 64 | 98 |
NFKAPPABcanonicalpathway (NCI) | 9 | 2 | 3 | 10 | 24 |
TRAF6 mediated induction of the antiviral cytokine IFN alpha beta cascade (REACTOME) | 10 | 7 | 6 | 30 | 53 |
Negative regulation of apoptosis (MsigDB) | 19 | 18 | 19 | 91 | 147 |
MAPK signaling pathway (KEGG) | 24 | 34 | 34 | 175 | 267 |
Signaling in immune system (REACTOME) | 28 | 47 | 47 | 244 | 366 |
       Down-regulated | |||||
LSM1-7 complex (CORUM) | 4 | 2 | 1 | 0 | 7 |
Respiratory chain complex I (incomplete intermediate) mitochondrial (CORUM) | 4 | 3 | 4 | 0 | 11 |
Mitochondrial respiratory chain (MsigDB) | 8 | 7 | 7 | 2 | 24 |