[1] "disease_type: STAD-TP"
[1] "pheno.from.Aggregate_Molecular_Subtype_Clusters: TRUE"
[1] "pheno.name: mRNAseq_cNMF"
[1] "tcga.pheno.FileName: /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/15114286/STAD-TP.mergedcluster.txt"
[1] "tcga.exp.FileName: /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/STAD-TP/14527787/STAD-TP.mRNAseq_RPKM_log2.txt"
[1] "gs.db: /xchip/cga/reference/MSigDB/c2.cp.v3.0-2.symbols.gmt"
[1] "GSEA.v.1.0.reshuffling.type: sample.labels"
[1] "GSEA.v.1.0.nperm: 1000"
[1] "GSEA.v.1.0.weighted.score.type: 1"
[1] "GSEA.v.1.0.nom.p.val.threshold: -1"
[1] "GSEA.v.1.0.fwer.p.val.threshold: -1"
[1] "GSEA.v.1.0.fdr.q.val.threshold: 0.25"
[1] "GSEA.v.1.0.topgs: 20"
[1] "GSEA.v.1.0.adjust.FDR.q.val: FALSE"
[1] "GSEA.v.1.0.gs.size.threshold.min: 25"
[1] "GSEA.v.1.0.gs.size.threshold.max: 500"
[1] "GSEA.v.1.0.reverse.sign: FALSE"
[1] "GSEA.v.1.0.perm.type: 0"
[1] "R version 3.0.1 (2013-05-16)"
[1] "1.1. prepare phenotype data"
[1] "read phenotype data:  mRNAseq_cNMF  in aggregate molecuar subtype clusters"
[1] "pheno.type: 1 - 5 :[  clus1  ]  66"
[1] "class.pheno"
[1] "clus1"     "NON.clus1"
[1] "pheno.type: 2 - 5 :[  clus2  ]  63"
[1] "class.pheno"
[1] "clus2"     "NON.clus2"
[1] "pheno.type: 3 - 5 :[  clus3  ]  46"
[1] "class.pheno"
[1] "clus3"     "NON.clus3"
[1] "pheno.type: 4 - 5 :[  clus4  ]  37"
[1] "class.pheno"
[1] "clus4"     "NON.clus4"
[1] "pheno.type: 5 - 5 :[  clus5  ]  62"
[1] "class.pheno"
[1] "clus5"     "NON.clus5"
[1] "generated input phenotype - clusterInfo data..."
[1] "1.2. prepare expression data"
[1] "generated input expression data..."
[1] "1.3. load input gs.db data..."
[1] "2. start running GSEA for each cluster..."
[1] "#***** cluster:[  1  ] -  5"
[1] "dir [  STAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway/  ] created..."
[1] " *** Running GSEA Analysis..."
[1] "# Copy input parameters to log file"
[1] "# Start of GSEA methodology"
[1] "# Read input data matrix..."
[1] "# Read input class vector..."
[1] "# Read input gene set database"
[1] "Number of genes:" "22643"           
[1] "Number of Gene Sets:" "195"                 
[1] "Number of samples:" "274"               
[1] "Original number of Gene Sets:" "404"                          
[1] "Maximum gene set size:" "388"                   
[1] "# basic_data_info file"
[1] "# Read gene and gene set annotations if gene annotation file was provided"
[1] "# Compute observed and random permutation gene rankings"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  1 -- 100"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  101 -- 200"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  201 -- 300"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  301 -- 400"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  401 -- 500"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  501 -- 600"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  601 -- 700"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  701 -- 800"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  801 -- 900"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  901 -- 1000"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing observed enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing observed enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing observed enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing observed enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing observed enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing observed enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing observed enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing observed enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing observed enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing observed enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing observed enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing observed enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing observed enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing observed enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing observed enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing observed enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing observed enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing observed enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing observed enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing observed enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing observed enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing observed enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing observed enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing observed enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing observed enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing observed enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing observed enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing observed enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing observed enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing observed enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing observed enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing observed enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing observed enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing observed enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing observed enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing observed enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing observed enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing observed enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing observed enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing observed enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing observed enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing observed enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing observed enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing observed enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing observed enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing observed enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing observed enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing observed enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing observed enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing observed enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing observed enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing observed enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing observed enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing observed enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing observed enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing observed enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing observed enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing observed enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing observed enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing observed enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing observed enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing observed enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing observed enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing observed enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing observed enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing observed enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing observed enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing observed enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing observed enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing observed enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing observed enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing observed enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing observed enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing observed enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing observed enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing observed enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing observed enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing observed enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing observed enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing observed enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing observed enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing observed enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing observed enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing observed enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing observed enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing observed enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing observed enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing observed enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing observed enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing observed enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing observed enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing observed enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing observed enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing observed enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing observed enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing observed enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing observed enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing observed enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing observed enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing observed enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing observed enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing observed enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing observed enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing observed enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing observed enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing observed enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing observed enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing observed enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing observed enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing observed enrichment for gene set: 195 WNT_SIGNALING"
[1] "# Compute enrichment for random permutations"
[1] "Computing random permutations' enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing random permutations' enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing random permutations' enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing random permutations' enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing random permutations' enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing random permutations' enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing random permutations' enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing random permutations' enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing random permutations' enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing random permutations' enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing random permutations' enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing random permutations' enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing random permutations' enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing random permutations' enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing random permutations' enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing random permutations' enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing random permutations' enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing random permutations' enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing random permutations' enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing random permutations' enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing random permutations' enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing random permutations' enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing random permutations' enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing random permutations' enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing random permutations' enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing random permutations' enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing random permutations' enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing random permutations' enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing random permutations' enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing random permutations' enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing random permutations' enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing random permutations' enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing random permutations' enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing random permutations' enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing random permutations' enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing random permutations' enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing random permutations' enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing random permutations' enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing random permutations' enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing random permutations' enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing random permutations' enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing random permutations' enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing random permutations' enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing random permutations' enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing random permutations' enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing random permutations' enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing random permutations' enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing random permutations' enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing random permutations' enrichment for gene set: 195 WNT_SIGNALING"
[1] "0gene sets out of 195GS has NA values in GSEA.results$ES score"
integer(0)
[1] "# Compute 3 types of p-values"
[1] "Computing nominal p-values..."
[1] "Computing rescaling normalization for each gene set null..."
[1] "# Save intermedite results"
[1] "Computing FWER p-values..."
[1] "Computing FDR q-values..."
[1] "# adjust q-values"
[1] "# Compute global statistic"
[1] "Producing result tables and plots..."
[1] "global plot - 1.Gene List Correlation (S2N) Profile plot"
[1] "# plot S2N correlation profile"
[1] "global plot - 2.Global Observed and Null Densities (Area Normalized) plot"
[1] -0.002730155  0.009100517  0.009100517  0.009041370  0.009100517
[1] "global plot - 3.Heat Map for Genes in Dataset plot"
[1] "GSEA.HeatMapPlot()"
[1] "global plot - 4.p-values vs. NES plot"
[1] "# p-vals plot"
[1] "generate files of sig.genes and fold-change up/down genes"
[1] "generated .significant.genes.txt"
[1] "generated .up.regulated.genes.txt and .down.regulated.genes.txt"
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "#***** cluster:[  2  ] -  5"
[1] "dir [  STAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway/  ] created..."
[1] " *** Running GSEA Analysis..."
[1] "# Copy input parameters to log file"
[1] "# Start of GSEA methodology"
[1] "# Read input data matrix..."
[1] "# Read input class vector..."
[1] "# Read input gene set database"
[1] "Number of genes:" "22643"           
[1] "Number of Gene Sets:" "195"                 
[1] "Number of samples:" "274"               
[1] "Original number of Gene Sets:" "404"                          
[1] "Maximum gene set size:" "388"                   
[1] "# basic_data_info file"
[1] "# Read gene and gene set annotations if gene annotation file was provided"
[1] "# Compute observed and random permutation gene rankings"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  1 -- 100"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  101 -- 200"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  201 -- 300"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  301 -- 400"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  401 -- 500"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  501 -- 600"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  601 -- 700"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  701 -- 800"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  801 -- 900"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  901 -- 1000"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing observed enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing observed enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing observed enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing observed enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing observed enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing observed enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing observed enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing observed enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing observed enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing observed enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing observed enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing observed enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing observed enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing observed enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing observed enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing observed enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing observed enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing observed enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing observed enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing observed enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing observed enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing observed enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing observed enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing observed enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing observed enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing observed enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing observed enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing observed enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing observed enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing observed enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing observed enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing observed enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing observed enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing observed enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing observed enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing observed enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing observed enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing observed enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing observed enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing observed enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing observed enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing observed enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing observed enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing observed enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing observed enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing observed enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing observed enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing observed enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing observed enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing observed enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing observed enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing observed enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing observed enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing observed enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing observed enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing observed enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing observed enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing observed enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing observed enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing observed enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing observed enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing observed enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing observed enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing observed enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing observed enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing observed enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing observed enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing observed enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing observed enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing observed enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing observed enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing observed enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing observed enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing observed enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing observed enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing observed enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing observed enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing observed enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing observed enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing observed enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing observed enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing observed enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing observed enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing observed enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing observed enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing observed enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing observed enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing observed enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing observed enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing observed enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing observed enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing observed enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing observed enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing observed enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing observed enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing observed enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing observed enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing observed enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing observed enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing observed enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing observed enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing observed enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing observed enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing observed enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing observed enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing observed enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing observed enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing observed enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing observed enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing observed enrichment for gene set: 195 WNT_SIGNALING"
[1] "# Compute enrichment for random permutations"
[1] "Computing random permutations' enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing random permutations' enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing random permutations' enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing random permutations' enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing random permutations' enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing random permutations' enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing random permutations' enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing random permutations' enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing random permutations' enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing random permutations' enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing random permutations' enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing random permutations' enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing random permutations' enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing random permutations' enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing random permutations' enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing random permutations' enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing random permutations' enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing random permutations' enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing random permutations' enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing random permutations' enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing random permutations' enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing random permutations' enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing random permutations' enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing random permutations' enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing random permutations' enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing random permutations' enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing random permutations' enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing random permutations' enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing random permutations' enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing random permutations' enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing random permutations' enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing random permutations' enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing random permutations' enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing random permutations' enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing random permutations' enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing random permutations' enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing random permutations' enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing random permutations' enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing random permutations' enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing random permutations' enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing random permutations' enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing random permutations' enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing random permutations' enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing random permutations' enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing random permutations' enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing random permutations' enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing random permutations' enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing random permutations' enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing random permutations' enrichment for gene set: 195 WNT_SIGNALING"
[1] "0gene sets out of 195GS has NA values in GSEA.results$ES score"
integer(0)
[1] "# Compute 3 types of p-values"
[1] "Computing nominal p-values..."
[1] "Computing rescaling normalization for each gene set null..."
[1] "# Save intermedite results"
[1] "Computing FWER p-values..."
[1] "Computing FDR q-values..."
[1] "# adjust q-values"
[1] "# Compute global statistic"
[1] "Producing result tables and plots..."
[1] "global plot - 1.Gene List Correlation (S2N) Profile plot"
[1] "# plot S2N correlation profile"
[1] "global plot - 2.Global Observed and Null Densities (Area Normalized) plot"
[1] -0.002732149  0.009107162  0.009107162  0.009107162  0.008311982
[1] "global plot - 3.Heat Map for Genes in Dataset plot"
[1] "GSEA.HeatMapPlot()"
[1] "global plot - 4.p-values vs. NES plot"
[1] "# p-vals plot"
[1] "generate files of sig.genes and fold-change up/down genes"
[1] "generated .significant.genes.txt"
[1] "generated .up.regulated.genes.txt and .down.regulated.genes.txt"
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "#***** cluster:[  3  ] -  5"
[1] "dir [  STAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway/  ] created..."
[1] " *** Running GSEA Analysis..."
[1] "# Copy input parameters to log file"
[1] "# Start of GSEA methodology"
[1] "# Read input data matrix..."
[1] "# Read input class vector..."
[1] "# Read input gene set database"
[1] "Number of genes:" "22643"           
[1] "Number of Gene Sets:" "195"                 
[1] "Number of samples:" "274"               
[1] "Original number of Gene Sets:" "404"                          
[1] "Maximum gene set size:" "388"                   
[1] "# basic_data_info file"
[1] "# Read gene and gene set annotations if gene annotation file was provided"
[1] "# Compute observed and random permutation gene rankings"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  1 -- 100"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  101 -- 200"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  201 -- 300"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  301 -- 400"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  401 -- 500"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  501 -- 600"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  601 -- 700"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  701 -- 800"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  801 -- 900"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  901 -- 1000"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing observed enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing observed enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing observed enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing observed enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing observed enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing observed enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing observed enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing observed enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing observed enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing observed enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing observed enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing observed enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing observed enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing observed enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing observed enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing observed enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing observed enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing observed enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing observed enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing observed enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing observed enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing observed enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing observed enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing observed enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing observed enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing observed enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing observed enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing observed enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing observed enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing observed enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing observed enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing observed enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing observed enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing observed enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing observed enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing observed enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing observed enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing observed enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing observed enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing observed enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing observed enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing observed enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing observed enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing observed enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing observed enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing observed enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing observed enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing observed enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing observed enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing observed enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing observed enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing observed enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing observed enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing observed enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing observed enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing observed enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing observed enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing observed enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing observed enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing observed enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing observed enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing observed enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing observed enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing observed enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing observed enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing observed enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing observed enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing observed enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing observed enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing observed enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing observed enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing observed enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing observed enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing observed enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing observed enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing observed enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing observed enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing observed enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing observed enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing observed enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing observed enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing observed enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing observed enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing observed enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing observed enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing observed enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing observed enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing observed enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing observed enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing observed enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing observed enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing observed enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing observed enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing observed enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing observed enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing observed enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing observed enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing observed enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing observed enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing observed enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing observed enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing observed enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing observed enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing observed enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing observed enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing observed enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing observed enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing observed enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing observed enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing observed enrichment for gene set: 195 WNT_SIGNALING"
[1] "# Compute enrichment for random permutations"
[1] "Computing random permutations' enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing random permutations' enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing random permutations' enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing random permutations' enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing random permutations' enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing random permutations' enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing random permutations' enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing random permutations' enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing random permutations' enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing random permutations' enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing random permutations' enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing random permutations' enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing random permutations' enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing random permutations' enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing random permutations' enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing random permutations' enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing random permutations' enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing random permutations' enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing random permutations' enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing random permutations' enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing random permutations' enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing random permutations' enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing random permutations' enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing random permutations' enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing random permutations' enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing random permutations' enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing random permutations' enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing random permutations' enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing random permutations' enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing random permutations' enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing random permutations' enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing random permutations' enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing random permutations' enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing random permutations' enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing random permutations' enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing random permutations' enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing random permutations' enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing random permutations' enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing random permutations' enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing random permutations' enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing random permutations' enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing random permutations' enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing random permutations' enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing random permutations' enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing random permutations' enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing random permutations' enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing random permutations' enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing random permutations' enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing random permutations' enrichment for gene set: 195 WNT_SIGNALING"
[1] "0gene sets out of 195GS has NA values in GSEA.results$ES score"
integer(0)
[1] "# Compute 3 types of p-values"
[1] "Computing nominal p-values..."
[1] "Computing rescaling normalization for each gene set null..."
[1] "# Save intermedite results"
[1] "Computing FWER p-values..."
[1] "Computing FDR q-values..."
[1] "# adjust q-values"
[1] "# Compute global statistic"
[1] "Producing result tables and plots..."
[1] "global plot - 1.Gene List Correlation (S2N) Profile plot"
[1] "# plot S2N correlation profile"
[1] "global plot - 2.Global Observed and Null Densities (Area Normalized) plot"
[1] -0.002908817  0.009696058  0.009696058  0.009172621  0.009696058
[1] "global plot - 3.Heat Map for Genes in Dataset plot"
[1] "GSEA.HeatMapPlot()"
[1] "global plot - 4.p-values vs. NES plot"
[1] "# p-vals plot"
[1] "generate files of sig.genes and fold-change up/down genes"
[1] "generated .significant.genes.txt"
[1] "generated .up.regulated.genes.txt and .down.regulated.genes.txt"
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "#***** cluster:[  4  ] -  5"
[1] "dir [  STAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway/  ] created..."
[1] " *** Running GSEA Analysis..."
[1] "# Copy input parameters to log file"
[1] "# Start of GSEA methodology"
[1] "# Read input data matrix..."
[1] "# Read input class vector..."
[1] "# Read input gene set database"
[1] "Number of genes:" "22643"           
[1] "Number of Gene Sets:" "195"                 
[1] "Number of samples:" "274"               
[1] "Original number of Gene Sets:" "404"                          
[1] "Maximum gene set size:" "388"                   
[1] "# basic_data_info file"
[1] "# Read gene and gene set annotations if gene annotation file was provided"
[1] "# Compute observed and random permutation gene rankings"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  1 -- 100"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  101 -- 200"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  201 -- 300"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  301 -- 400"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  401 -- 500"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  501 -- 600"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  601 -- 700"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  701 -- 800"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  801 -- 900"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  901 -- 1000"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing observed enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing observed enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing observed enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing observed enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing observed enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing observed enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing observed enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing observed enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing observed enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing observed enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing observed enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing observed enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing observed enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing observed enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing observed enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing observed enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing observed enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing observed enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing observed enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing observed enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing observed enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing observed enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing observed enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing observed enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing observed enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing observed enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing observed enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing observed enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing observed enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing observed enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing observed enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing observed enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing observed enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing observed enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing observed enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing observed enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing observed enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing observed enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing observed enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing observed enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing observed enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing observed enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing observed enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing observed enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing observed enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing observed enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing observed enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing observed enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing observed enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing observed enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing observed enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing observed enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing observed enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing observed enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing observed enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing observed enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing observed enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing observed enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing observed enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing observed enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing observed enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing observed enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing observed enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing observed enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing observed enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing observed enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing observed enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing observed enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing observed enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing observed enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing observed enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing observed enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing observed enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing observed enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing observed enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing observed enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing observed enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing observed enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing observed enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing observed enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing observed enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing observed enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing observed enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing observed enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing observed enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing observed enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing observed enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing observed enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing observed enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing observed enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing observed enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing observed enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing observed enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing observed enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing observed enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing observed enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing observed enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing observed enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing observed enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing observed enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing observed enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing observed enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing observed enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing observed enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing observed enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing observed enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing observed enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing observed enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing observed enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing observed enrichment for gene set: 195 WNT_SIGNALING"
[1] "# Compute enrichment for random permutations"
[1] "Computing random permutations' enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing random permutations' enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing random permutations' enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing random permutations' enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing random permutations' enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing random permutations' enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing random permutations' enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing random permutations' enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing random permutations' enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing random permutations' enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing random permutations' enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing random permutations' enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing random permutations' enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing random permutations' enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing random permutations' enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing random permutations' enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing random permutations' enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing random permutations' enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing random permutations' enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing random permutations' enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing random permutations' enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing random permutations' enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing random permutations' enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing random permutations' enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing random permutations' enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing random permutations' enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing random permutations' enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing random permutations' enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing random permutations' enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing random permutations' enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing random permutations' enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing random permutations' enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing random permutations' enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing random permutations' enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing random permutations' enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing random permutations' enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing random permutations' enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing random permutations' enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing random permutations' enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing random permutations' enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing random permutations' enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing random permutations' enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing random permutations' enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing random permutations' enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing random permutations' enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing random permutations' enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing random permutations' enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing random permutations' enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing random permutations' enrichment for gene set: 195 WNT_SIGNALING"
[1] "0gene sets out of 195GS has NA values in GSEA.results$ES score"
integer(0)
[1] "# Compute 3 types of p-values"
[1] "Computing nominal p-values..."
[1] "Computing rescaling normalization for each gene set null..."
[1] "# Save intermedite results"
[1] "Computing FWER p-values..."
[1] "Computing FDR q-values..."
[1] "# adjust q-values"
[1] "# Compute global statistic"
[1] "Producing result tables and plots..."
[1] "global plot - 1.Gene List Correlation (S2N) Profile plot"
[1] "# plot S2N correlation profile"
[1] "global plot - 2.Global Observed and Null Densities (Area Normalized) plot"
[1] -0.002791854  0.009306178  0.009306178  0.009306178  0.008104244
[1] "global plot - 3.Heat Map for Genes in Dataset plot"
[1] "GSEA.HeatMapPlot()"
[1] "global plot - 4.p-values vs. NES plot"
[1] "# p-vals plot"
[1] "generate files of sig.genes and fold-change up/down genes"
[1] "generated .significant.genes.txt"
[1] "generated .up.regulated.genes.txt and .down.regulated.genes.txt"
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "#***** cluster:[  5  ] -  5"
[1] "dir [  STAD-TP-mRNAseq_cNMF-clus5___Class2-CanonicalPathway/  ] created..."
[1] " *** Running GSEA Analysis..."
[1] "# Copy input parameters to log file"
[1] "# Start of GSEA methodology"
[1] "# Read input data matrix..."
[1] "# Read input class vector..."
[1] "# Read input gene set database"
[1] "Number of genes:" "22643"           
[1] "Number of Gene Sets:" "195"                 
[1] "Number of samples:" "274"               
[1] "Original number of Gene Sets:" "404"                          
[1] "Maximum gene set size:" "388"                   
[1] "# basic_data_info file"
[1] "# Read gene and gene set annotations if gene annotation file was provided"
[1] "# Compute observed and random permutation gene rankings"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  1 -- 100"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  101 -- 200"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  201 -- 300"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  301 -- 400"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  401 -- 500"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  501 -- 600"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  601 -- 700"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  701 -- 800"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  801 -- 900"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing ranked list for actual and permuted phenotypes.......permutations:  901 -- 1000"
[1] "run GSEA.GeneRanking..."
[1] "random/proportional PERMUTATION sampling.......r in nperms:  100  permutation.type:  random (unbalanced) permutation"
[1] "Computing observed enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing observed enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing observed enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing observed enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing observed enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing observed enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing observed enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing observed enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing observed enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing observed enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing observed enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing observed enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing observed enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing observed enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing observed enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing observed enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing observed enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing observed enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing observed enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing observed enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing observed enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing observed enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing observed enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing observed enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing observed enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing observed enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing observed enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing observed enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing observed enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing observed enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing observed enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing observed enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing observed enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing observed enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing observed enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing observed enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing observed enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing observed enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing observed enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing observed enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing observed enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing observed enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing observed enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing observed enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing observed enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing observed enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing observed enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing observed enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing observed enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing observed enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing observed enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing observed enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing observed enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing observed enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing observed enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing observed enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing observed enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing observed enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing observed enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing observed enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing observed enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing observed enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing observed enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing observed enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing observed enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing observed enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing observed enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing observed enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing observed enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing observed enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing observed enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing observed enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing observed enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing observed enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing observed enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing observed enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing observed enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing observed enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing observed enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing observed enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing observed enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing observed enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing observed enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing observed enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing observed enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing observed enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing observed enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing observed enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing observed enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing observed enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing observed enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing observed enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing observed enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing observed enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing observed enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing observed enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing observed enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing observed enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing observed enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing observed enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing observed enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing observed enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing observed enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing observed enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing observed enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing observed enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing observed enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing observed enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing observed enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing observed enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing observed enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing observed enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing observed enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing observed enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing observed enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing observed enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing observed enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing observed enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing observed enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing observed enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing observed enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing observed enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing observed enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing observed enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing observed enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing observed enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing observed enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing observed enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing observed enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing observed enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing observed enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing observed enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing observed enrichment for gene set: 195 WNT_SIGNALING"
[1] "# Compute enrichment for random permutations"
[1] "Computing random permutations' enrichment for gene set: 1 BIOCARTA_NO1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 2 BIOCARTA_AGR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 3 BIOCARTA_ALK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 4 BIOCARTA_AT1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 5 BIOCARTA_BCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 6 BIOCARTA_BIOPEPTIDES_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 7 BIOCARTA_CARM_ER_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 8 BIOCARTA_G1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 9 BIOCARTA_HDAC_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 10 BIOCARTA_INFLAM_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 11 BIOCARTA_EGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 12 BIOCARTA_ERK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 13 BIOCARTA_FAS_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 14 BIOCARTA_FCER1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 15 BIOCARTA_FMLP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 16 BIOCARTA_GH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 17 BIOCARTA_HIVNEF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 18 BIOCARTA_MPR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 19 BIOCARTA_IL2RB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 20 BIOCARTA_GSK3_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 21 BIOCARTA_DEATH_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 22 BIOCARTA_RACCYCD_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 23 BIOCARTA_INTEGRIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 24 BIOCARTA_KERATINOCYTE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 25 BIOCARTA_PYK2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 26 BIOCARTA_MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 27 BIOCARTA_PPARA_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 28 BIOCARTA_VIP_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 29 BIOCARTA_NFAT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 30 BIOCARTA_P38MAPK_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 31 BIOCARTA_PDGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 32 BIOCARTA_EDG1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 33 BIOCARTA_MYOSIN_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 34 BIOCARTA_CHREBP2_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 35 BIOCARTA_RHO_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 36 BIOCARTA_NKT_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 37 BIOCARTA_IL1R_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 38 BIOCARTA_MET_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 39 BIOCARTA_GPCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 40 BIOCARTA_TCR_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 41 BIOCARTA_PAR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 42 BIOCARTA_TNFR1_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 43 BIOCARTA_TOLL_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 44 BIOCARTA_CREB_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 45 BIOCARTA_VEGF_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 46 KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 47 KEGG_CITRATE_CYCLE_TCA_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 48 KEGG_PENTOSE_PHOSPHATE_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 49 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 50 KEGG_GALACTOSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 51 KEGG_FATTY_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 52 KEGG_STEROID_HORMONE_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 53 KEGG_OXIDATIVE_PHOSPHORYLATION"
[1] "Computing random permutations' enrichment for gene set: 54 KEGG_PURINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 55 KEGG_PYRIMIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 56 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 57 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 58 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 59 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 60 KEGG_LYSINE_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 61 KEGG_ARGININE_AND_PROLINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 62 KEGG_HISTIDINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 63 KEGG_TYROSINE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 64 KEGG_TRYPTOPHAN_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 65 KEGG_SELENOAMINO_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 66 KEGG_GLUTATHIONE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 67 KEGG_STARCH_AND_SUCROSE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 68 KEGG_N_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 69 KEGG_O_GLYCAN_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 70 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 71 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE"
[1] "Computing random permutations' enrichment for gene set: 72 KEGG_GLYCEROLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 73 KEGG_INOSITOL_PHOSPHATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 74 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 75 KEGG_ETHER_LIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 76 KEGG_ARACHIDONIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 77 KEGG_LINOLEIC_ACID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 78 KEGG_SPHINGOLIPID_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 79 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
[1] "Computing random permutations' enrichment for gene set: 80 KEGG_PYRUVATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 81 KEGG_PROPANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 82 KEGG_BUTANOATE_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 83 KEGG_RETINOL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 84 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM"
[1] "Computing random permutations' enrichment for gene set: 85 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
[1] "Computing random permutations' enrichment for gene set: 86 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 87 KEGG_DRUG_METABOLISM_CYTOCHROME_P450"
[1] "Computing random permutations' enrichment for gene set: 88 KEGG_DRUG_METABOLISM_OTHER_ENZYMES"
[1] "Computing random permutations' enrichment for gene set: 89 KEGG_ABC_TRANSPORTERS"
[1] "Computing random permutations' enrichment for gene set: 90 KEGG_RIBOSOME"
[1] "Computing random permutations' enrichment for gene set: 91 KEGG_RNA_DEGRADATION"
[1] "Computing random permutations' enrichment for gene set: 92 KEGG_RNA_POLYMERASE"
[1] "Computing random permutations' enrichment for gene set: 93 KEGG_BASAL_TRANSCRIPTION_FACTORS"
[1] "Computing random permutations' enrichment for gene set: 94 KEGG_DNA_REPLICATION"
[1] "Computing random permutations' enrichment for gene set: 95 KEGG_SPLICEOSOME"
[1] "Computing random permutations' enrichment for gene set: 96 KEGG_PROTEASOME"
[1] "Computing random permutations' enrichment for gene set: 97 KEGG_PPAR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 98 KEGG_BASE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 99 KEGG_NUCLEOTIDE_EXCISION_REPAIR"
[1] "Computing random permutations' enrichment for gene set: 100 KEGG_HOMOLOGOUS_RECOMBINATION"
[1] "Computing random permutations' enrichment for gene set: 101 KEGG_MAPK_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 102 KEGG_ERBB_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 103 KEGG_CALCIUM_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 104 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 105 KEGG_CHEMOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 106 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM"
[1] "Computing random permutations' enrichment for gene set: 107 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 108 KEGG_CELL_CYCLE"
[1] "Computing random permutations' enrichment for gene set: 109 KEGG_OOCYTE_MEIOSIS"
[1] "Computing random permutations' enrichment for gene set: 110 KEGG_P53_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 111 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
[1] "Computing random permutations' enrichment for gene set: 112 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
[1] "Computing random permutations' enrichment for gene set: 113 KEGG_LYSOSOME"
[1] "Computing random permutations' enrichment for gene set: 114 KEGG_ENDOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 115 KEGG_PEROXISOME"
[1] "Computing random permutations' enrichment for gene set: 116 KEGG_MTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 117 KEGG_APOPTOSIS"
[1] "Computing random permutations' enrichment for gene set: 118 KEGG_CARDIAC_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 119 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION"
[1] "Computing random permutations' enrichment for gene set: 120 KEGG_WNT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 121 KEGG_NOTCH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 122 KEGG_HEDGEHOG_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 123 KEGG_TGF_BETA_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 124 KEGG_AXON_GUIDANCE"
[1] "Computing random permutations' enrichment for gene set: 125 KEGG_VEGF_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 126 KEGG_FOCAL_ADHESION"
[1] "Computing random permutations' enrichment for gene set: 127 KEGG_ECM_RECEPTOR_INTERACTION"
[1] "Computing random permutations' enrichment for gene set: 128 KEGG_CELL_ADHESION_MOLECULES_CAMS"
[1] "Computing random permutations' enrichment for gene set: 129 KEGG_ADHERENS_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 130 KEGG_TIGHT_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 131 KEGG_GAP_JUNCTION"
[1] "Computing random permutations' enrichment for gene set: 132 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES"
[1] "Computing random permutations' enrichment for gene set: 133 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
[1] "Computing random permutations' enrichment for gene set: 134 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 135 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 136 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 137 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 138 KEGG_JAK_STAT_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 139 KEGG_HEMATOPOIETIC_CELL_LINEAGE"
[1] "Computing random permutations' enrichment for gene set: 140 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY"
[1] "Computing random permutations' enrichment for gene set: 141 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 142 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 143 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 144 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
[1] "Computing random permutations' enrichment for gene set: 145 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION"
[1] "Computing random permutations' enrichment for gene set: 146 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION"
[1] "Computing random permutations' enrichment for gene set: 147 KEGG_LONG_TERM_POTENTIATION"
[1] "Computing random permutations' enrichment for gene set: 148 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 149 KEGG_LONG_TERM_DEPRESSION"
[1] "Computing random permutations' enrichment for gene set: 150 KEGG_OLFACTORY_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 151 KEGG_TASTE_TRANSDUCTION"
[1] "Computing random permutations' enrichment for gene set: 152 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON"
[1] "Computing random permutations' enrichment for gene set: 153 KEGG_INSULIN_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 154 KEGG_GNRH_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 155 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION"
[1] "Computing random permutations' enrichment for gene set: 156 KEGG_MELANOGENESIS"
[1] "Computing random permutations' enrichment for gene set: 157 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY"
[1] "Computing random permutations' enrichment for gene set: 158 KEGG_TYPE_II_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 159 KEGG_TYPE_I_DIABETES_MELLITUS"
[1] "Computing random permutations' enrichment for gene set: 160 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 161 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
[1] "Computing random permutations' enrichment for gene set: 162 KEGG_ALZHEIMERS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 163 KEGG_PARKINSONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 164 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
[1] "Computing random permutations' enrichment for gene set: 165 KEGG_HUNTINGTONS_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 166 KEGG_PRION_DISEASES"
[1] "Computing random permutations' enrichment for gene set: 167 KEGG_VIBRIO_CHOLERAE_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 168 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 169 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 170 KEGG_LEISHMANIA_INFECTION"
[1] "Computing random permutations' enrichment for gene set: 171 KEGG_PATHWAYS_IN_CANCER"
[1] "Computing random permutations' enrichment for gene set: 172 KEGG_COLORECTAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 173 KEGG_RENAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 174 KEGG_PANCREATIC_CANCER"
[1] "Computing random permutations' enrichment for gene set: 175 KEGG_ENDOMETRIAL_CANCER"
[1] "Computing random permutations' enrichment for gene set: 176 KEGG_GLIOMA"
[1] "Computing random permutations' enrichment for gene set: 177 KEGG_PROSTATE_CANCER"
[1] "Computing random permutations' enrichment for gene set: 178 KEGG_THYROID_CANCER"
[1] "Computing random permutations' enrichment for gene set: 179 KEGG_BASAL_CELL_CARCINOMA"
[1] "Computing random permutations' enrichment for gene set: 180 KEGG_MELANOMA"
[1] "Computing random permutations' enrichment for gene set: 181 KEGG_BLADDER_CANCER"
[1] "Computing random permutations' enrichment for gene set: 182 KEGG_CHRONIC_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 183 KEGG_ACUTE_MYELOID_LEUKEMIA"
[1] "Computing random permutations' enrichment for gene set: 184 KEGG_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 185 KEGG_NON_SMALL_CELL_LUNG_CANCER"
[1] "Computing random permutations' enrichment for gene set: 186 KEGG_AUTOIMMUNE_THYROID_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 187 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS"
[1] "Computing random permutations' enrichment for gene set: 188 KEGG_ALLOGRAFT_REJECTION"
[1] "Computing random permutations' enrichment for gene set: 189 KEGG_GRAFT_VERSUS_HOST_DISEASE"
[1] "Computing random permutations' enrichment for gene set: 190 KEGG_PRIMARY_IMMUNODEFICIENCY"
[1] "Computing random permutations' enrichment for gene set: 191 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM"
[1] "Computing random permutations' enrichment for gene set: 192 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC"
[1] "Computing random permutations' enrichment for gene set: 193 KEGG_DILATED_CARDIOMYOPATHY"
[1] "Computing random permutations' enrichment for gene set: 194 KEGG_VIRAL_MYOCARDITIS"
[1] "Computing random permutations' enrichment for gene set: 195 WNT_SIGNALING"
[1] "0gene sets out of 195GS has NA values in GSEA.results$ES score"
integer(0)
[1] "# Compute 3 types of p-values"
[1] "Computing nominal p-values..."
[1] "Computing rescaling normalization for each gene set null..."
[1] "# Save intermedite results"
[1] "Computing FWER p-values..."
[1] "Computing FDR q-values..."
[1] "# adjust q-values"
[1] "# Compute global statistic"
[1] "Producing result tables and plots..."
[1] "global plot - 1.Gene List Correlation (S2N) Profile plot"
[1] "# plot S2N correlation profile"
[1] "global plot - 2.Global Observed and Null Densities (Area Normalized) plot"
[1] -0.003063884  0.010212945  0.010212945  0.009240393  0.010212945
[1] "global plot - 3.Heat Map for Genes in Dataset plot"
[1] "GSEA.HeatMapPlot()"
[1] "global plot - 4.p-values vs. NES plot"
[1] "# p-vals plot"
[1] "generate files of sig.genes and fold-change up/down genes"
[1] "generated .significant.genes.txt"
[1] "generated .up.regulated.genes.txt and .down.regulated.genes.txt"
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "volcano plot for each GS"
[1] "generated a volcano plot.pdf ."
[1] "generated a volcano plot.png ."
[1] "END!"
