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["Overview of the gene sets regulated in the stress relevant gene set collections in the antioxidant group when compared to controls. A brief description of each gene set is included with Pubmed id reference."]
["Gene set collection","Gene set (www.broadinstitute.org/gsea)","genes in gene set (n)","nom p value","FDR %","Brief description of gene sets"]
[null,"GNF2_APEX1",78,"<0.01","<0.01","Neighborhood of APEX1 in the GNF2 expression compendium (Broad Inst)"]
["DNA and repair","GCM_APEX1",106,"<0.01","<0.01","Neighborhood of APEX1 in the GCM expression compendium (Broad Inst)"]
[null,"MENSSEN_MYC_UP",26,"<0.01","<0.01","MYC target genes involved in DNA repair and cell cycle regulation  (Pubmed 11983916 )"]
[null,"UVC_XPCS_8HR_DN",371,"<0.01",0.5,"Down-regulated at 8 hours following treatment of XPB/CS fibroblasts with 3 J/m^2 UVC (Pubmed 15608684)"]
[null,"KANNAN_P53_DN",121,"<0.01",0.4,"Target genes down regulated by p53(Pubmed 11402317)"]
[null,"UVC_XPCS_ALL_DN",432,"<0.01",0.37,"Down-regulated at any timepoint following treatment of XPB/CS fibroblasts with 3 J/m^2 UVC (Pubmed 15608684)"]
[null,"DNA_REPAIR",15,"<0.01",0.52,"Genes annotated by the GO term GO:0006281. The process of restoring DNA after damage. (Pubmed 10802651)"]
[null,"H2O2_CSBDIFF_C2",33,"<0.01",0.98,"Deficient induction by H2O2 fibroblasts defective in transcription-coupled DNA repair base excision repair transcription and chromatin structural organization  (Pubmed 12606941)"]
[null,"NUCLEOTIDE_EXCISION_REPAIR",20,0.01,1.26,"Genes annotated by the GO term GO:0006289. (Pubmed 10802651)"]
[null,"UVC_TTD_4HR_DN",266,"<0.01",1.48,"Down-regulated at 4 hours following treatment of XPB/TTD fibroblasts with 3 J/m^2 UVC (Pubmed 15608684)"]
[null,"UVC_XPCS_4HR_DN",36,"<0.01",1.35,"Down-regulated at 4 hours following treatment of XPB/TTD fibroblasts with 3 J/m^2 UVC (Pubmed 15608684)"]
[null,"BRENTANI_REPAIR",210,0.01,1.48,"Cancer related genes involved in DNA repair  (Pubmed 14593198)"]
[null,"UVC_TTD_ALL_DN",325,"<0.01",1.72,"Down-regulated at any timepoint following treatment of XPB/TTD fibroblasts with 3 J/m^2 UVC (Pubmed 15608684)"]
[null,"UVC_TTD_8HR_DN",150,"<0.01",1.87,"Down-regulated at 8 hours following treatment of XPB/TTD fibroblasts with 3 J/m^2 UVC (Pubmed 15608684)"]
[null,"MMS_HUMAN_LYMPH_LOW_4HRS_DN",15,0.02,3.41,"Down-regulated following treatment of human lymphocytes (TK6) with methyl methanesulfonate (Pubmed 15515172)"]
[]
[null,"SCHUMACHER_MYC_UP",51,"<0.01",4.77,"Genes up-regulated by MYC in P493-6 (B-cell) (Pubmed 11139609 )"]
["Stress","ET743_SARCOMA_24HRS_DN",99,"<0.01",4.37,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"ET743_SARCOMA_DN",245,"<0.01",3.66,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"ET743_SARCOMA_48HRS_DN",171,"<0.01",2.78,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"ET743_SARCOMA_72HRS_DN",33,"<0.01",2.35,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"H2O2_CSBDIFF_C2",204,"<0.01",2.28,"Deficient induction by H2O2 fibroblasts defective in transcription-coupled DNA repair base excision repair transcription and chromatin structural organization  (Pubmed 12606941)"]
[]
["Oxidative and stress","SCHUMACHER_MYC_UP",51,"<0.01",1.43,"Genes up-regulated by MYC in P493-6 (B-cell) (Pubmed 11139609 )"]
[null,"H2O2_CSBDIFF_C2",33,"<0.01",1.89,"Deficient induction by H2O2 fibroblasts defective in transcription-coupled DNA repair base excision repair transcription and chromatin structural organization  (Pubmed 12606941)"]
[]
["Stress and response","ET743_SARCOMA_24HRS_DN",99,"<0.01",4.82,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"ET743_SARCOMA_48HRS_DN",171,"<0.01",2.49,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"ET743_SARCOMA_DN",245,"<0.01",2.09,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"ET743_SARCOMA_72HRS_DN",204,"<0.01",1.93,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[]
[null,"HYPOXIA_RCC_UP",92,"<0.01",1.59,"Upregulated by hypoxia in VHL-rescued renal carcinoma cells (Pubmed 12692265) "]
["Hypoxia","RCC_NL_UP",483,"<0.01",3.42,"Upregulated in VHL-rescued renal carcinoma vs. normal renal cells (Pubmed 12692265)"]
[null,"VHL_NORMAL_UP",407,"<0.01",3.76,"Upregulated in VHL-rescued renal carcinoma vs. normal renal cells (Pubmed 12692265)"]
[null,"MANALO_HYPOXIA_DN",75,0.01,4.65,"Genes downregulated in human pulmonary endothelial cells under hypoxic conditions or after exposure to AdCA5, an adenovirus carrying constitutively active hypoxia-inducible factor 1 (HIF-1alpha).( Pubmed 15374877 )"]
[null,"UVB_NHEK1_C1",52,"<0.01",0.32,"Upregulated by UV-B light in normal human epidermal keratinocytes.  Pubmed 12771951 "]
["Apoptosis","MORF_AATF",185,"<0.01",1.1,"Neighborhood of AATF apoptosis antagonizing transcription factor in the MORF expression compendium (Broad Inst)"]
[null,"CMV_HCMV_TIMECOURSE_18HRS_UP",71,"<0.01",2.15,"Regulated in fibroblasts following infection with human cytomegalovirus  (Pubmed 11711622)"]
[null,"KANNAN_P53_DN",15,0.01,3.23,"Target genes down regulated by p53(Pubmed 11402317)"]
[null,"ET743_SARCOMA_24HRS_DN",99,"<0.01",3.31,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"ET743_SARCOMA_DN",245,"<0.01",3.05,"Down-regulated in sarcoma cells after treatment with a marine . Cell cycle control, stress and DNA-damage response genes (Pubmed 15897246) "]
[null,"ET743_SARCOMA_48HRS_DN",171,"<0.01",3.11,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"ET743_SARCOMA_72HRS_DN",204,"<0.01",2.89,"Down-regulated after treatment with a marine anticancer agent in at least 8 of 11 sarcoma cell lines  (Pubmed 15897246) "]
[null,"UVC_HIGH_ALL_DN",273,"<0.01",3.89,"Down-regulated at any timepoint following treatment of WS1 human skin fibroblasts with UVC at a high dose (50 J/m^2)"]
[null,"UVB_NHEK1_C6",117,"<0.01",3.78,"Downregulated by UV-B light in normal human epidermal keratinocytes (Pubmed 12771951) (antiapoptotic and cell survival factors, growth factors and proinflammatory mediators and DNA repair-related genes)"]
[null,"TSA_HEPATOMA_CANCER_DN",15,"<0.01",4.37,"Cancer-related genes down-regulated in any of four human hepatoma cell lines following 24-hour treatment with 200ng/mL of trichostatin A (Pubmed 15452378 )"]
["Immune and response","CMV_HCMV_TIMECOURSE_18HRS_UP",71,0.45,1.99,"Regulated in fibroblasts following infection with human cytomegalovirus  (Pubmed 11711622)"]
["Cytokin*","CMV_HCMV_TIMECOURSE_18HRS_UP",71,"<0.01",4.03,"Regulated in fibroblasts following infection with human cytomegalovirus  (Pubmed 11711622)"]
["Inflammation","JISON_SICKLECELL_DIFF",329,"<0.01",4.08]
[{"$nulls":5},"Significantly differentially expressed genes in sickle cell patients. The 112 genes are involved in heme metabolism, cell-cycle regulation, antioxidant and stress responses, inflammation and angiogenesis. (Pubmed 15031206)"]
[]
["Interleukin","GNF2_IL2RB",43,"<0.01",4.37,"Neighborhood of IL2RB interleukin 2 receptor (Broad institute)"]

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