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Table 3 Summary of the GSEA-identified gene sets in in vitro activated T cells of psoriasis patients compared to healthy controls

From: Genome-wide transcriptional analysis of T cell activation reveals differential gene expression associated with psoriasis

Name NES NOM p-val FDR q-val
General processes of immune system    
Reactome cytokine signaling in immune system 2.498 0.000 0.0000
KEGG cytokine cytokine receptor interaction 1.980 0.000 0.0130
KEGG hematopoietic cell lineage 1.917 0.000 0.0167
KEGG cell adhesion molecules cams 1.903 0.000 0.0173
Infectious and autoimmune diseases    
KEGG autoimmune thyroid disease 1.996 0.002 0.0126
KEGG allograft rejection 1.866 0.000 0.0234
KEGG leishmania infection 1.961 0.000 0.0121
KEGG viral myocarditis 1.900 0.000 0.0175
T cell activation    
Reactome downstream TCR signaling 1.869 0.000 0.0232
PID NFAT TF pathway 1.903 0.000 0.0179
PID AP1 pathway 1.936 0.000 0.0148
Biocarta CTLA4 pathway 1.854 0.000 0.0253
Innate immune system activation    
Reactome innate immune system 2.145 0.000 0.0014
Reactome inflammasomes 1.905 0.000 0.0180
Reactome antiviral mechanism by IFN stimulated genes 1.915 0.000 0.0160
Reactome RIG I MDA5 mediated induction of IFN alpha beta pathways 2.212 0.000 0.0005
KEGG RIG I like receptor signaling pathway 2.144 0.000 0.0012
Reactome negative regulators of RIG I MDA5 signaling 2.123 0.000 0.0018
KEGG NOD like receptor signaling pathway 1.953 0.000 0.0128
Reactome nucleotide binding domain leucine rich repeat containing receptor NLR signaling pathways 2.048 0.000 0.0058
KEGG toll like receptor signaling pathway 1.802 0.000 0.0398
Reactome TRAF6 mediated IRF7 activation 1.875 0.002 0.0226
KEGG cytosolic DNA sensing pathway 1.781 0.002 0.0449
Cytokine signaling    
KEGG JAK STAT signaling pathway 1.977 0.000 0.0119
PID IL12 STAT4 pathway 1.775 0.004 0.0454
Reactome interferon signaling 2.701 0.000 0.0000
Reactome interferon alpha beta signaling 2.760 0.000 0.0000
Reactome interferon gamma signaling 2.303 0.000 0.0000
PID IFNG pathway 1.787 0.002 0.0434
PID SMAD2 3 nuclear pathway 2.094 0.000 0.0031
Reactome transcriptional activity OF SMAD2 SMAD3 SMAD4 heterotrimer 1.794 0.002 0.0421
Reactome SMAD2 SMAD3 SMAD4 heterotrimer regulates transcription 1.771 0.012 0.0451
Differentiation, proliferation and apoptosis    
PID notch pathway 1.916 0.000 0.0163
PID Betacatenin Nuc pathway 1.844 0.002 0.0271
Biocarta gleevec pathway 1.862 0.000 0.0237
PID CMYB pathway 1.842 0.000 0.0271
Reactome YAP1 AND WWTR1 TAZ stimulated gene expression 1.804 0.008 0.0400
PID P53 downstream pathway 1.772 0.000 0.0452
Metabolism    
Reactome cholesterol biosynthesis 2.050 0.000 0.0063
Reactome fatty acid triacylglycerol and ketone body metabolism 1.961 0.000 0.0128
Reactome metabolism of lipids and lipoproteins 1.927 0.000 0.0157
KEGG biosynthesis of unsaturated fatty acids 1.790 0.006 0.0429
KEGG glycine serine and threonine metabolism 1.877 0.000 0.0227
KEGG metabolism of xenobiotics by cytochrome P450 1.924 0.002 0.0157
Reactome PPARA activates gene expression 2.076 0.000 0.0043
Biocarta PPARA pathway 1.780 0.006 0.0444
Unfolded protein response    
Reactome unfolded protein response 1.972 0.000 0.0120
Reactome perk regulated gene expression 1.872 0.000 0.0230
Reactome activation of genes by ATF4 1.896 0.000 0.0180
PID ATF2 pathway 1.977 0.000 0.0125
Other    
KEGG intestinal immune network for IGA production 1.996 0.000 0.0117
KEGG lysosome 1.951 0.000 0.0127
Reactome generic transcription pathway 1.813 0.000 0.0372
PID HIF1 TFPATHWAY 1.778 0.002 0.0444
Reactome RORA activates circadian expression 1.773 0.007 0.0457
  1. List of the enriched gene sets in psoriasis phenotype compared to control phenotype showing a FDR < 0.05. Gene sets are classified according to the processes where they are involved. Normalized enrichment score (NES), nominal p-value (NOM p-value) and false discovery rate (FDR q-value) are indicated.