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Table 4 A selection of significantly impacted pathways (BioCarta) in T lymphocytes following IL-2 deprivation.

From: Molecular signature of cell cycle exit induced in human T lymphoblasts by IL-2 withdrawal

Pathway description Biocarta Pathway LS permutation
p-value
KS permutation
p-value
Efron-Tibshirani's GSA test p-value Up-regulated genes
(p < 0.01)
Down-regulated genes
(p < 0.01)
Visceral Fat Deposits and the Metabolic Syndrome h_vobesityPathway 0.00001 0.0001273 < 0.005 NR3C1 TNF, HSD11B1
Cells and Molecules involved in local acute inflammatory response h_LairPathway 0.00001 0.0007952 < 0.005 ITGB1, ITGAL IL8, TNF, ICAM1, ITGA4
Adhesion and Diapedesis of Lymphocytes h_lympathway 0.00001 0.0029985 < 0.005 ITGB1, ITGAL IL8, ICAM1, ICAM2, ITGA4
Adhesion and Diapedesis of Granulocytes h_granulocytesPathway 0.00001 0.0032844 < 0.005   IL-8, TNF, CD54, ICAM2
Cytokine Network h_cytokinePathway 0.00001 0.0297027 < 0.005   IL13, IL8, LTA, IL-5
IL-2 Receptor Beta Chain in T cell Activation h_il2rbPathway 0.00001 0.030315 < 0.005   CISH, IL2RA, SOCS3, BCL2, AKT1, JAK3
Induction of apoptosis through DR3 and DR4/5 Death Receptors h_deathPathway 0.00001 0.00001 0.06   BCL2, TRADD
IL22 Soluble Receptor Signaling Pathway h_il22bppathway 0.0000955 0.00001 < 0.005   SOCS3, JAK3
Selective expression of chemokine receptors during T-cell polarization h_nktPathway 0.0000994 0.0000936 0.03 IL12RB1, CCR4 ILRB2, CCL3, IL5
Cytokines and Inflammatory Response h_inflamPathway 0.0001717 0.078942 < 0.005   IL13, IL8, TNF, LTA, IL5
NO2-dependent IL 12 Pathway in NK cells h_no2il12Pathway 0.0006013 0.0135205 < 0.005 IL12RB1, CD2 IL12RB2
Regulation of MAP Kinase Pathways Through Dual Specificity Phosphatases h_dspPathway 0.0007988 0.1717258 < 0.005   DUSP6, DUSP1
PTEN dependent cell cycle arrest and apoptosis h_ptenPathway 0.0015749 0.0100088 < 0.005 FOXO3, ITGB1, MAPK1 AKT1, PDK1, SOS1
Ceramide Signaling Pathway h_ceramidePathway 0.0016286 0.005673 < 0.005 MAPK1 BCL2, TRADD
Th1/Th2 Differentiation h_th1th2Pathway 0.001734 0.0676275 0.07 IL12RB1 IL2RA, IL12RB2
Dendritic cells in regulating TH1 and TH2 Development h_dcPathway 0.0023595 0.0493208 < 0.005   
p53 Signaling Pathway h_p53Pathway 0.0026524 0.1802796 < 0.005   BCL2, CDK2, CDKN1A
Telomeres, Telomerase, Cellular Aging, and Immortality h_telPathway 0.0367325 0.3499152 < 0.005   BCL2, AKT1
Phospholipids as signalling intermediaries h_edg1Pathway 0.0404929 0.1894782 < 0.005 ASAH1 AKT1
  1. Testing of 288 Biocarta human pathways identified 54 out of 288 investigated gene-sets that passed the 0.005 significance threshold in at least one test (38 gene-sets in LS/KS test and 36 in Efron-Tibshirani's test).