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

Table 6 Enriched gene sets other than involved in energy production

Gene set name	VvsB_CD8	VvsB_CD4	VvL_CD8	VvL_CD4	BvsL_CD4
Cell cycle and apoptosis related
CHEMICALPATHWAY	0.1		0.1
APOPTOSIS		0.1		0.1
APOPTOSIS_GENMAPP		0.1
CASPASEPATHWAY				0.1	0.05
SA_CASPASE_CASCADE					0.05
DNA_REPLICATION_REACTOME	0.05		0.05		0.1
G1_TO_S_CELL_CYCLE_REACTOME	0.05
HSA04110_CELL_CYCLE	0.05
CELL_CYCLE_KEGG	0.05
CELLCYCLEPATHWAY	0.05
G2PATHWAY	0.1
G1PATHWAY	0.1
P53PATHWAY	0.1
MPRPATHWAY	0.1
ST_GA12_PATHWAY		0.05
Cytotoxicity, complement activation and cell signalling
HSA04612_ANTIGEN_PROCESSING_AND_PRESENTATION	0.05	0.05	0.05
HSA04650_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY	0.05	0.05		0.05
COMPPATHWAY		0.05		0.05	0.05
HSA04610_Complement_and_coagulation-cascades		0.05		0.05
INTRINSICPATHWAY		0.1		0.1
HSA04620_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY		0.05		0.1
TOLLPATHWAY		0.05
HSA04662_B_CELL_RECEPTOR_SIGNALING_PATHWAY		0.1
SA_B_CELL_RECEPTOR_COMPLEXES		0.1
Cytoskeleton and cell adhesion
RHOPATHWAY	0.05		0.05	0.05	0.05
NDKDYNAMINPATHWAY	0.1
SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES			0.1
INTEGRIN_MEDIATED_CELL_ADHESION_KEGG		0.1
Interleukin
IL12PATHWAY	0.1
NO2IL12PATHWAY	0.1
TIDPATHWAY		0.1
IL6PATHWAY		0.1
IL3PATHWAY		0.1
Other
SPPAPATHWAY		0.1
HSA05120_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION		0.05
HSA05131_PATHOGENIC_ESCHERICHIA_COLI_INFECTION_EPEC		0.1
HSA05130_PATHOGENIC_ESCHERICHIA_COLI_INFECTION_EHEC		0.1
HSA04320_DORSO_VENTRAL_AXIS_FORMATION		0.1
HSA05219_BLADDER_CANCER		0.1

VvsB_CD8: Gene sets enriched in the VIR group in the comparison of VIR versus BDL in CD8+ T cells
VvsB_CD4: Gene sets enriched in the VIR group in the comparison of VIR versus BDL in CD4+ T cells
VvL_CD8: Gene sets enriched in the VIR group in the comparison of VIR versus LTNP in CD8+ T cells
VvL_CD4: Gene sets enriched in the VIR group in the comparison of VIR versus LTNP in CD4+ T cells
BvsL_CD4: Gene sets enriched in the BDL group in the comparison of BDL versus LTNP in CD4+ T cells
Gene sets significantly enriched are marked by the number 0.05 or 0.1 in the corresponding paired comparisons 0.05: FDR < or = 0.05; 0.1: FDR < or = 0.1
Gene set information could be searched at the website http://www.broad.mit.edu/gsea/msigdb/search.jsp

ISSN: 1742-4690