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Table 5 Enriched gene sets involved in energy production

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 VvsB_CD8 VvsB_CD4 VvL_CD8 VvL_CD4 BvsL_CD4
Aerobic metabolism      
HSA00190_OXIDATIVE_PHOSPHORYLATION 0.05 0.05 0.05 0.05 0.05
HSA00020_CITRATE_CYCLE 0.1 0.1 0.1   0.1
HSA00760_NICOTINATE_AND_NICOTINAMIDE_METABOLISM 0.05 0.05 0.1 0.05  
TYPE_III_SECRETION_SYSTEM   0.05   0.05 0.05
PHOTOSYNTHESIS   0.05   0.05 0.05
ATP_SYNTHESIS   0.05   0.05 0.05
FLAGELLAR_ASSEMBLY   0.05   0.05 0.05
MITOCHONDRIAL_FATTY_ACID_BETAOXIDATION 0.1    0.1  
PYRUVATE_METABOLISM    0.1   0.05
Carbohydrate and lipid metabolism      
HSA00650_BUTANOATE_METABOLISM 0.05 0.1   0.05 0.05
HSA00071_FATTY_ACID_METABOLISM 0.05    0.05 0.05
HSA00670_ONE_CARBON_POOL_BY_FOLATE 0.1    0.1 0.1
HSA00051_FRUCTOSE_AND_MANNOSE_METABOLISM 0.1 0.1   0.1  
HSA00511_N_GLYCAN_DEGRADATION   0.05   0.05 0.1
HSA00030_PENTOSE_PHOSPHATE_PATHWAY 0.1    0.1  
HSA01032_GLYCAN_STRUCTURES_DEGRADATION   0.05   0.05  
STARCH_AND_SUCROSE_METABOLISM   0.05   0.1  
HSA00052_GALACTOSE_METABOLISM   0.1 0.1   
HSA00532_CHONDROITIN_SULFATE_BIOSYNTHESIS   0.1   0.05  
PROPANOATE_METABOLISM 0.05     
HSA00040_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.1     
HSA00010_GLYCOLYSIS_AND_GLUCONEOGENESIS 0.1     
GLYCOLYSIS 0.1     
GLUCONEOGENESIS 0.1     
HSA00710_CARBON_FIXATION     0.1  
PROSTAGLANDIN_AND_LEUKOTRIENE_METABOLISM     0.1  
BILE_ACID_BIOSYNTHESIS      0.05
HSA00531_GLYCOSAMINOGLYCAN_DEGRADATION   0.1    
HSA00565_ETHER_LIPID_METABOLISM   0.1    
FRUCTOSE_AND_MANNOSE_METABOLISM   0.1    
Amino acid and nucleotide metabolism      
HSA00280_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.05 0.1 0.05 0.05 0.05
LYSINE_DEGRADATION 0.05   0.1 0.05 0.05
HSA00230_PURINE_METABOLISM 0.05 0.1 0.1 0.1  
PHENYLALANINE_METABOLISM   0.1 0.05 0.05 0.1
HSA00380_TRYPTOPHAN_METABOLISM   0.1 0.1 0.05 0.1
HSA00240_PYRIMIDINE_METABOLISM 0.05 0.1   0.05  
HSA00252_ALANINE_AND_ASPARTATE_METABOLISM 0.1    0.1 0.05
HSA00410_BETA_ALANINE_METABOLISM 0.05    0.1  
PORPHYRIN_AND_CHLOROPHYLL_METABOLISM 0.05 0.1   0.05 0.1
HSA00330_ARGININE_AND_PROLINE_METABOLISM     0.1  
Protein metabolism      
PROTEASOME 0.05 0.1 0.05 0.05 0.05
PROTEASOMEPATHWAY   0.1   0.1 0.1
HSA00970_AMINOACYL_TRNA_BIOSYNTHESIS 0.05    0.1  
  1. The presence of curious gene groups photosynthesis, Type III secretion and flagellar assembly is due to the heavy overlapping genes between these pathways and OXPHOS pathway we have found significant in our study. For example, in the group comparison, VIR versus BDL in CD4 T cells, 53 core enrichment genes contributed to the enrichment of OXPHOS pathway and 10 core enrichment genes contributed to the flagellar assembly pathway. All these 10 core genes from flagellar assembly pathway ATP6V1D, ATP6V0D1, ATP6V1A, ATP6V0A1, ATP6V1B2, ATP6AP1, ATP6V1E1, ATP6V1H, ATP6V0B, and ATP6V1F are ALL present in the 53 core genes from OXPHOS pathway. In this overlapping situation, when you do Gene Set Enrichment Analysis (GSEA) using the gene set file (gmt file constructed by gene symbols downloaded from broad institute website), the flagellar pathway will appear together with OXPHOS pathway as the same gene symbol applies to different species and these 2 pathways do have a number of overlapping genes. It is common that at the level of pathway analysis, pathways with certain amount of overlapping genes will always appear together, just like flagellar assembly showed up with the OXPHOS. Our results just reflected the true output from GSEA analysis. We leave them there but at the bottom of the aerobic metabolism category with the consideration that it reflects the same biological theme related to ATP production even though from different species.
  2. VvsB_CD8: Gene sets enriched in the VIR group in the comparison of VIR versus BDL in CD8+ T cells
  3. VvsB_CD4: Gene sets enriched in the VIR group in the comparison of VIR versus BDL in CD4+ T cells
  4. VvL_CD8: Gene sets enriched in the VIR group in the comparison of VIR versus LTNP in CD8+ T cells
  5. VvL_CD4: Gene sets enriched in the VIR group in the comparison of VIR versus LTNP in CD4+ T cells
  6. BvsL_CD4: Gene sets enriched in the BDL group in the comparison of BDL versus LTNP in CD4+ T cells
  7. 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
  8. Gene set information could be searched at the website http://www.broad.mit.edu/gsea/msigdb/search.jsp