Skip to main content

Advertisement

Table 2 GSEA GSA results

From: Investigating the effect of paralogs on microarray gene-set analysis

Original dataset: unique GSA results Reduced dataset: unique GSA results
[1] Lymphoblast cell lines: [1] Lymphoblast cell lines:
   - Enriched in males:    -Enriched in males:
   TGFBETA_C2_UP    CROONQUIST_IL6_STROMA_UP
   -Enriched in females:    -Enriched in females:
     CHESLER_HIGHEST_FOLD_RANGE_GENES BHATTACHARYA_ESC_UP
[2] p53 status in NCI-60 cell lines: [2] p53 status in NCI-60 cell lines:
   -Enriched in p53 wild type:    -Enriched in p53 wild type:
   P53HYPOXIAPATHWAY  
   HSP27PATHWAY  
   MMS_HUMAN_LYMPH_HIGH_24HRS_UP  
   P53PATHWAY  
   KANNAN_P53_UP  
   P53_BRCA_UP  
   RADIATION_SENSITIVITY  
[3] Acute leukaemias: [3] Acute leukaemias:
   -Enriched in ALL:    -Enriched in ALL:
     chr13q14
[4] Lung cancer outcome (Boston study): [4] Lung cancer outcome (Boston study):
   -Enriched in poor outcome:    -Enriched in poor outcome:
   TGFBETA_C1_UP HDACLCOLON_TSA_DN    CANCER_UNDIFFERENTIATED_META_UP
     MARSHALL_SPLEEN_BAL
     TRNASYNTHETASES
     EGF_HDMEC_UP
     AMINOACYL-TRNA_BIOSYNTHESIS
     ZELLER_MYC_UP
     HDACI_COLON_BUT16HRS_DN
     ZHAN_MULTIPLE_MYELOMA_SUBCLASSES_DIFF
     MYC_TARGETS
     MENSE_HYPOXIA_UP
     SMITH_HTERT_UP
     DOX_RESIST_GASTRIC_UP
     BASSO_REGULATORY_HUBS
[5] Lung cancer outcome (Michigan study): [5] Lung cancer outcome (Michigan study):
   -Enriched in poor outcome:    -Enriched in poor outcome:
   TGFBETA_C1_UP  
   HSA00010_GLYCOLYSIS_AND_GLUCONEOGENESIS  
   GLYCOLYSIS GLUCONEOGENESIS  
   MENSE_HYPOXIA_UP  
   VEGFPATHWAY  
   ROME_INSULIN_2F_UP  
   INSULIN-SIGNALING  
   BHATTACHARYA_ESC_UP  
   VANTVEER_BREAST_OUTCOME_GOOD_VS_POOR_DN  
   GLYCOLYSIS_AND_GLUCONEOGENESIS  
   ZUCCHI_EPITHELIAL_DN  
   HYPOXIA_REVIEW  
  1. GSEA results of five diverse gene expression datasets showing gene sets significantly enriched in the phenotype indicated. Functional gene sets (MSigDB:C2) were used in all cases, except for the leukaemia dataset where cytogenetic gene sets (MSigDB:C1) were used. Only those sets exclusive to the results obtained from either the original or paralog-reduced list are shown. A threshold of FDR ≤ 0.25 was used to determine significance.