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Table 3 Consistently perturbed gene sets

From: Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions

Gene set | AC| | A C| | C A| |AC| | 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
  1. The columns from left to right are: (i) gene set name, (ii) |A C|: the number of genes in the gene set perturbed by both A. fumigatus and C. albicans, (iii) |A C|: the number of genes perturbed by A. fumigatus but not by C. albicans, (iv) |C A|: the number of genes perturbed by C. albicans but not by A. fumigatus, (v) |A C|: the number of genes unperturbed by both pathogens, and (vi) |n|: the total number of genes in a gene set. For each gene set, we have indicated the source database in parentheses. This table shows gene sets that have a McNemar’s test statistic value of zero.