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Table 7 Enriched pathways in CD4+ T cells from the LTNP group (BDL versus LTNP)

From: Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease

Gene set name Gene set size NES NOM p-val FDR
MAPK pathway associated     
NTHIPATHWAY 22 -2.05 0.000 0.008
ST_JNK_MAPK_PATHWAY 40 -1.88 0.002 0.038
ST_GRANULE_CELL_SURVIVAL_PATHWAY 26 -1.77 0.002 0.049
IGF1PATHWAY 20 -1.77 0.002 0.049
INSULINPATHWAY 21 -1.79 0.004 0.050
NGFPATHWAY 19 -1.81 0.002 0.053
CARDIACEGFPATHWAY 17 -1.75 0.000 0.056
41BBPATHWAY 18 -1.74 0.014 0.058
CDMACPATHWAY 16 -1.71 0.010 0.073
HSA04012_ERBB_SIGNALING_PATHWAY 87 -1.70 0.008 0.074
SA_TRKA_RECEPTOR 16 -1.70 0.012 0.075
HSA04010_MAPK_SIGNALING_PATHWAY 256 -1.64 0.000 0.087
PDGFPATHWAY 27 -1.66 0.012 0.088
TPOPATHWAY 23 -1.66 0.012 0.089
EGFPATHWAY 27 -1.66 0.018 0.091
Cell signaling     
INFLAMPATHWAY 29 -1.99 0.000 0.017
CYTOKINEPATHWAY 20 -1.95 0.000 0.023
CCR5PATHWAY 18 -1.78 0.006 0.049
TCRPATHWAY 43 -1.80 0.006 0.052
IL6PATHWAY 21 -1.79 0.002 0.054
IL1RPATHWAY 32 -1.82 0.000 0.055
IL12PATHWAY 20 -1.68 0.018 0.083
TOLLPATHWAY 34 -1.66 0.012 0.086
HSA04060_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 253 -1.65 0.000 0.087
HSA04660_T_CELL_RECEPTOR_SIGNALING_PATHWAY 93 -1.65 0.006 0.089
CALCINEURIN_NF_AT_SIGNALING 92 -1.92 0.000 0.030
Other     
HYPERTROPHY_MODEL 17 -1.91 0.000 0.025
ATMPATHWAY 19 -1.86 0.000 0.043
HSA05210_COLORECTAL_CANCER 85 -1.78 0.000 0.049
SMOOTH_MUSCLE_CONTRACTION 140 -1.83 0.000 0.051
CIRCADIAN_EXERCISE 40 -1.79 0.000 0.051
GPCRPATHWAY 35 -1.76 0.006 0.054
ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS 42 -1.73 0.002 0.064
P53HYPOXIAPATHWAY 19 -1.68 0.022 0.082
  1. Gene set size: number of genes in a particular gene set; NES: normalized enrichment score;
  2. NOM p-val: nominal p value; FDR: false discovery rate
  3. Gene set information could be searched at the website http://www.broad.mit.edu/gsea/msigdb/search.jsp