Beginning AltAnalyze Analysis... Format: non-log AltAnalyze version 2.1.4 - Expression Analysis Parameters Being Used... database: EnsMart72 species: Hs method: RNASeq manufacturer: RNASeq probability_statistic: moderated t-test constitutive_source: Ensembl dabg_p: 1.0 junction expression threshold: 5.0 exon_exp_threshold: 5.0 gene_exp_threshold: 200.0 exon_rpkm_threshold: 0.5 gene_rpkm_threshold: 1.0 exclude low expressing exons for RPKM: no avg_all_for_ss: yes expression_data_format: non-log include_raw_data: no run_from_scratch: Process RNA-seq reads perform_alt_analysis: expression calculate_gene_expression_using: core Alternative Exon Analysis Parameters Being Used... analysis_method: NA p_threshold: NA filter_data_types: NA alt_exon_fold_variable: NA gene_expression_cutoff: NA remove_intronic_junctions: NA avg_all_for_ss: yes permute_p_threshold: NA perform_permutation_analysis: NA export_NI_values: no run_MiDAS: no use_direct_domain_alignments_only: no microRNA_prediction_method: any analyze_all_conditions: pairwise filter_for_AS: no run_GOElite: run-immediately Using AltDatabase/kallisto/0.43.1/PC/bin/kallisto.exe Running kallisto on: CO_42_POS_DMSO_83562_S2 ... completed in 522 seconds Running kallisto on: CO_42_NEG_DMSO_83561_S1 ... completed in 603 seconds ...Performing analyses on Kallisto-TPM values directly. Beginning to process the Hs gene-level dataset Adding additional gene, GO and WikiPathways annotations * * * * * * * * * ArrayID annotations imported in 1 seconds 0 Array IDs with annotations from RNASeq annotation files imported. Processing the expression file: C:/Users/Brian/Desktop/CORR/test_output/ExpressionInput/exp.NEW_test.txt 36963 IDs imported...beginning to calculate statistics for all group comparisons GroupStats instance has no attribute 'n1' 1|1.3222258609 Moderated test failed due to issue with mpmpath or out-of-range values ... using unmoderated unpaired test instead! * * * * * * * * * * Ensembl-Affymetrix relationships imported 63194 Ensembl Biotypes and 9 housekeeping genes. Full Dataset with statistics: DATASET-NEW_test.txt written Exported GO-Elite input files... Examining: DATASET-NEW_test.txt Examining: COUNTS-NEW_test.txt 382 genes with data to export... Export inputs for clustering to: C:/Users/Brian/Desktop/CORR/test_output/ExpressionOutput/Clustering/SampleLogFolds-NEW_test.txt Export summary gene expression results to: SUMMARY-NEW_test.txt Building quality control graphs... Dataset import in 0.2 seconds Building hierarchical cluster graphs... 382 rows and 2 columns imported for SampleLogFolds-NEW_test in 0.0 seconds... Performing Principal Component Analysis... Re-importing PCA model scores rather than calculating from scratch C:/Users/Brian/Desktop/CORR/test_output/DataPlots/SampleLogFolds-NEW_test-PCA_scores.txt ...no existing score file found exporting PCA loading genes to: C:/Users/Brian/Desktop/CORR/test_output/DataPlots//PCA/correlated.txt max allowed cluster size: 7000 Performing hieararchical clustering using cosine for columns and cosine for rows Column clustering completed in 0.0 seconds Row clustering completed in 0.0 seconds Beginning to run GO-Elite analysis on all results Running GO-Elite version 1.2.6 Primary GO-Elite Parameters commandLineMode: yes species: Hs results-directory: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite//clustering/SampleLogFolds-NEW_test filter_method: z-score z_threshold: 1.96 p_val_threshold: 0.005 change_threshold: 2 sort_only_by_zscore: yes analysis_method: non-UI Heatmap criterion_input_folder: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite//clustering/SampleLogFolds-NEW_test custom_sets_folder: enrichment_type: ORA ORA Parameters mod: Ensembl permutations: FisherExactTest resources_to_analyze: GeneOntology UPDATED PARAMETERS - Forcing ORA algorithm to be FisherExactTest (required with no supplied denominator) Pruning c1-GO.txt * * * * * * * * * * Imported GeneOntology tree-structure for pruning 64 and 121 edges in the iGraph network. Pruning c2-GO.txt c2-GO.sif too large to visualize... gene associations assigned Wikipathways output in 0 seconds Dataset name: c2 267: Reported Filtered GO-terms 73: Reported Elite GO-terms 24: Elite GO-terms redundant with other Elite GO-terms 0: Reported Filtered Pathways 0: Filtered Pathways redundant with other Filtered Pathways 156: Number of genes associated with Filtered GO-terms 133: Number of genes associated with Elite GO-terms 0: Number of genes associated with Filtered Pathways Analysis completed in 29 seconds... Exiting GO-Elite 0 rows and 2 columns imported for OutlierLogFolds-NEW_test in 0.0 seconds... max allowed cluster size: 7000 SKIPPING HIERARCHICAL CLUSTERING!!! - Your dataset file has no associated rows. 382 rows and 2 columns imported for RelativeSampleLogFolds-NEW_test in 0.0 seconds... max allowed cluster size: 7000 Performing hieararchical clustering using cosine for columns and cosine for rows Column clustering completed in 0.0 seconds Row clustering completed in 0.0 seconds Beginning to run GO-Elite analysis on all results Running GO-Elite version 1.2.6 Primary GO-Elite Parameters commandLineMode: yes species: Hs results-directory: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite//clustering/RelativeSampleLogFolds-NEW_test filter_method: z-score z_threshold: 1.96 p_val_threshold: 0.005 change_threshold: 2 sort_only_by_zscore: yes analysis_method: non-UI Heatmap criterion_input_folder: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite//clustering/RelativeSampleLogFolds-NEW_test custom_sets_folder: enrichment_type: ORA ORA Parameters mod: Ensembl permutations: FisherExactTest resources_to_analyze: GeneOntology UPDATED PARAMETERS - Forcing ORA algorithm to be FisherExactTest (required with no supplied denominator) Pruning c1-GO.txt * * * * * * * * * * Imported GeneOntology tree-structure for pruning 64 and 121 edges in the iGraph network. Pruning c2-GO.txt c2-GO.sif too large to visualize... gene associations assigned Wikipathways output in 0 seconds Dataset name: c2 267: Reported Filtered GO-terms 73: Reported Elite GO-terms 24: Elite GO-terms redundant with other Elite GO-terms 0: Reported Filtered Pathways 0: Filtered Pathways redundant with other Filtered Pathways 156: Number of genes associated with Filtered GO-terms 133: Number of genes associated with Elite GO-terms 0: Number of genes associated with Filtered Pathways Analysis completed in 30 seconds... Exiting GO-Elite Converting values to log2... Converting values to normalized z-scores... 36963 rows and 2 columns imported for exp.NEW_test in 3.0 seconds... Performing Principal Component Analysis (please be patient)... Performing Principal Component Analysis... Re-importing PCA model scores rather than calculating from scratch C:/Users/Brian/Desktop/CORR/test_output/DataPlots/exp.NEW_test-PCA_scores.txt ...no existing score file found exporting PCA loading genes to: C:/Users/Brian/Desktop/CORR/test_output/DataPlots//PCA/correlated.txt Biological data type to examine: protein_coding Importing the tissue compedium database: Hs_exon_tissue-specific_protein_coding.txt 3946 genes in the tissue compendium database Importing the tissue compedium database: Hs_exon_tissue-specific_protein_coding.txt 3946 genes in the tissue compendium database importing: exp.NEW_test.txt 3850 matching genes in the dataset and tissue compendium database Beginning LineageProfiler analysis * * * * * * * * * * * * * * * * Correlation analysis finished LineageCorrelations-NEW_test-protein_coding-exon.txt exported... 114 rows and 2 columns imported for LineageCorrelations-NEW_test-protein_coding-zscores in 0.0 seconds... LineageProfiler analysis completed in 3.6 seconds Export inputs for clustering to: C:/Users/Brian/Desktop/CORR/test_output///ExpressionOutput/Clustering/LineageCorrelations-NEW_test-protein_coding-zscores-groups.txt 114 rows and 2 columns imported for LineageCorrelations-NEW_test-protein_coding-zscores in 0.0 seconds... max allowed cluster size: 7000 Performing hieararchical clustering using cosine for columns and cosine for rows Column clustering completed in 0.0 seconds Row clustering completed in 0.4 seconds 29 rows and 2 columns imported for LineageCorrelations-NEW_test-protein_coding-zscores-groups_filtered in 0.0 seconds... max allowed cluster size: 7000 Performing hieararchical clustering using cosine for columns and cosine for rows Column clustering completed in 0.0 seconds Row clustering completed in 0.0 seconds Coloring LineageMap profiles using WikiPathways webservice... This webservice appears to no longer be supported. Export 36963 rows to: C:/Users/Brian/Desktop/CORR/test_output/ExpressionOutput//AVERAGE-NEW_test.txt * * * * * * * * * * * * * * * * * * exported: C:/Users/Brian/Desktop/CORR/test_output/ExpressionOutput/MarkerFinder/MarkerGenes-ReplicateBased.txt 120 genes with data to export... Export inputs for clustering to: C:/Users/Brian/Desktop/CORR/test_output///ExpressionOutput/MarkerFinder/Clustering/MarkerGenes_correlations-ReplicateBased.txt 120 rows and 2 columns imported for MarkerGenes_correlations-ReplicateBased in 0.0 seconds... max allowed cluster size: 50000 Performing hieararchical clustering using euclidean for columns and cosine for rows Beginning to run GO-Elite analysis on all results Running GO-Elite version 1.2.6 Primary GO-Elite Parameters commandLineMode: yes species: Hs results-directory: C:/Users/Brian/Desktop/CORR/test_output//GO-Elite/MarkerFinder//clustering/MarkerGenes_correlations-ReplicateBased filter_method: z-score z_threshold: 1.96 p_val_threshold: 0.005 change_threshold: 2 sort_only_by_zscore: yes analysis_method: non-UI Heatmap criterion_input_folder: C:/Users/Brian/Desktop/CORR/test_output//GO-Elite/MarkerFinder//clustering/MarkerGenes_correlations-ReplicateBased custom_sets_folder: enrichment_type: ORA ORA Parameters mod: Ensembl permutations: FisherExactTest resources_to_analyze: GeneOntology UPDATED PARAMETERS - Forcing ORA algorithm to be FisherExactTest (required with no supplied denominator) Pruning cluster-42NEG-GO.txt * * * * * * * * * * Imported GeneOntology tree-structure for pruning 0 and 0 edges in the iGraph network. Pruning cluster-42POS-GO.txt 0 and 0 edges in the iGraph network. gene associations assigned Wikipathways output in 0 seconds Dataset name: cluster-42POS 0: Reported Filtered GO-terms 0: Reported Elite GO-terms 0: Elite GO-terms redundant with other Elite GO-terms 0: Reported Filtered Pathways 0: Filtered Pathways redundant with other Filtered Pathways 0: Number of genes associated with Filtered GO-terms 0: Number of genes associated with Elite GO-terms 0: Number of genes associated with Filtered Pathways Analysis completed in 28 seconds... Exiting GO-Elite Species: Hs | Algorithm: direct | InputType: IDs | IncludeExpIDs: True Genes: OntologyID: None Selected Interaction Files: WikiPathways KEGG TFTargets C:/Program Files/AltAnalyze_v.2.1.4.1-Win64/AltDatabase/EnsMart72/goelite/Hs/gene-interactions/Ensembl-WikiPathways.txt C:/Program Files/AltAnalyze_v.2.1.4.1-Win64/AltDatabase/EnsMart72/goelite/Hs/gene-interactions/Ensembl-KEGG.txt C:/Program Files/AltAnalyze_v.2.1.4.1-Win64/AltDatabase/EnsMart72/goelite/Hs/gene-interactions/Ensembl-TFTargets.txt Parsing interactions from: Ensembl-WikiPathways.txt Parsing interactions from: Ensembl-KEGG.txt Parsing interactions from: Ensembl-TFTargets.txt Imported interactions: 47552 Number of IDs from C:/Users/Brian/Desktop/CORR/test_output///GO-Elite/regulated//GE.42POS_vs_42NEG-fold2.0_rawp0.05.txt is 383 Number of IDs from C:/Users/Brian/Desktop/CORR/test_output///GO-Elite/regulated//GE.42POS_vs_42NEG-fold2.0_rawp0.05.txt is 383 Length of query_interactions: 30 Interaction data exported 25 and 22 edges in the iGraph network. Results saved to: C:/Users/Brian/Desktop/CORR/test_output///GO-Elite/regulated//networks/AltAnalyze-network-WKT_GE.42POS_vs_42NEG-fold2.0_rawp0.05-interactions_direct.png Beginning to run GO-Elite analysis on alternative exon results Running GO-Elite version 1.2.6 Primary GO-Elite Parameters commandLineMode: yes species: Hs results-directory: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite/regulated filter_method: z-score z_threshold: 1.96 p_val_threshold: 0.05 change_threshold: 2 sort_only_by_zscore: yes analysis_method: non-UI criterion_input_folder: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite/regulated custom_sets_folder: enrichment_type: ORA ORA Parameters mod: Ensembl permutations: FisherExactTest resources_to_analyze: all 250 edges and 210 Ontology annotations imported for biological_process 70 edges and 281 Ontology annotations imported for molecular_function 175 edges and 454 Ontology annotations imported for cellular_component 16110 edges and 10114 Ontology annotations imported for Diseases Ontology categories imported and nested in 2 seconds * * * * * * * * * * AltDatabase/goelite//Hs/nested/Ensembl_to_Nested-CTDOntology.txt saved to disk * * * * * * * * * * AltDatabase/goelite//Hs/nested/EntrezGene_to_Nested-CTDOntology.txt saved to disk Ontology categories imported and nested in 0 seconds * * * * * * * * * * AltDatabase/goelite//Hs/nested/Ensembl_to_Nested-GOSlim.txt saved to disk * * * * * * * * * * AltDatabase/goelite//Hs/nested/EntrezGene_to_Nested-GOSlim.txt saved to disk Ontology categories imported and nested in 0 seconds * * * * * * * * * * AltDatabase/goelite//Hs/nested/Ensembl_to_Nested-MPhenoOntology.txt saved to disk * * * * * * * * * * AltDatabase/goelite//Hs/nested/EntrezGene_to_Nested-MPhenoOntology.txt saved to disk Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-RVista_TFsites.txt 176 and 570 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-KEGG.txt 62 and 87 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-GOSlim.txt * * * * * * * * * * Imported GOSlim tree-structure for pruning 173 and 335 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-TFTargets.txt 44 and 41 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-HumanImmuneCells.txt 122 and 159 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-CTDOntology.txt * * * * * * * * * * Imported CTDOntology tree-structure for pruning 83 and 268 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-BioTypes.txt 54 and 53 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-Cardiac_TF_Targets.txt 69 and 79 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-PathwayCommons.txt 41 and 85 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-BioMarkers.txt GE.42POS_vs_42NEG-fold2.0_rawp0.05-BioMarkers.sif too large to visualize... Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-microRNATargets.txt 0 and 0 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-MergedTFTargets.txt 83 and 165 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-GO.txt * * * * * * * * * * Imported GeneOntology tree-structure for pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-GO.sif too large to visualize... Pruning GE.42POS_vs_42NEG-fold2.0_rawp0.05-local.txt 93 and 130 edges in the iGraph network. gene associations assigned Wikipathways output in 0 seconds Dataset name: GE.42POS_vs_42NEG-fold2.0_rawp0.05 518: Reported Filtered GO-terms 159: Reported Elite GO-terms 40: Elite GO-terms redundant with other Elite GO-terms 22: Reported Filtered Pathways 2: Filtered Pathways redundant with other Filtered Pathways 219: Number of genes associated with Filtered GO-terms 202: Number of genes associated with Elite GO-terms 71: Number of genes associated with Filtered Pathways Analysis completed in 142 seconds... Exiting GO-Elite Running GO-Elite version 1.2.6 Primary GO-Elite Parameters commandLineMode: yes species: Hs results-directory: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite/upregulated filter_method: z-score z_threshold: 1.96 p_val_threshold: 0.05 change_threshold: 2 sort_only_by_zscore: yes analysis_method: non-UI criterion_input_folder: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite/upregulated custom_sets_folder: enrichment_type: ORA ORA Parameters mod: Ensembl permutations: FisherExactTest resources_to_analyze: all Ontology categories imported and nested in 0 seconds * * * * * * * * * * AltDatabase/goelite//Hs/nested/Ensembl_to_Nested-MPhenoOntology.txt saved to disk * * * * * * * * * * AltDatabase/goelite//Hs/nested/EntrezGene_to_Nested-MPhenoOntology.txt saved to disk Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-RVista_TFsites.txt GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-RVista_TFsites.sif too large to visualize... Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-KEGG.txt 60 and 75 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-GOSlim.txt * * * * * * * * * * Imported GOSlim tree-structure for pruning 131 and 254 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-TFTargets.txt 28 and 27 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-HumanImmuneCells.txt 104 and 142 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-CTDOntology.txt * * * * * * * * * * Imported CTDOntology tree-structure for pruning 66 and 180 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-BioTypes.txt 40 and 39 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-Cardiac_TF_Targets.txt 55 and 58 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-PathwayCommons.txt 59 and 145 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-BioMarkers.txt GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-BioMarkers.sif too large to visualize... Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-microRNATargets.txt 25 and 24 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-MergedTFTargets.txt 124 and 223 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-GO.txt * * * * * * * * * * Imported GeneOntology tree-structure for pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-GO.sif too large to visualize... Pruning GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05-local.txt 76 and 103 edges in the iGraph network. gene associations assigned Wikipathways output in 0 seconds Dataset name: GE.42POS_vs_42NEG-upregulated-fold2.0_rawp0.05 458: Reported Filtered GO-terms 122: Reported Elite GO-terms 45: Elite GO-terms redundant with other Elite GO-terms 20: Reported Filtered Pathways 0: Filtered Pathways redundant with other Filtered Pathways 162: Number of genes associated with Filtered GO-terms 147: Number of genes associated with Elite GO-terms 56: Number of genes associated with Filtered Pathways Analysis completed in 225 seconds... Exiting GO-Elite Running GO-Elite version 1.2.6 Primary GO-Elite Parameters commandLineMode: yes species: Hs results-directory: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite/downregulated filter_method: z-score z_threshold: 1.96 p_val_threshold: 0.05 change_threshold: 2 sort_only_by_zscore: yes analysis_method: non-UI criterion_input_folder: C:/Users/Brian/Desktop/CORR/test_output/GO-Elite/downregulated custom_sets_folder: enrichment_type: ORA ORA Parameters mod: Ensembl permutations: FisherExactTest resources_to_analyze: all Ontology categories imported and nested in 0 seconds * * * * * * * * * * AltDatabase/goelite//Hs/nested/Ensembl_to_Nested-MPhenoOntology.txt saved to disk * * * * * * * * * * AltDatabase/goelite//Hs/nested/EntrezGene_to_Nested-MPhenoOntology.txt saved to disk Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-RVista_TFsites.txt 26 and 26 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-KEGG.txt 0 and 0 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-GOSlim.txt * * * * * * * * * * Imported GOSlim tree-structure for pruning 34 and 42 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-TFTargets.txt 0 and 0 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-HumanImmuneCells.txt 35 and 38 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-CTDOntology.txt * * * * * * * * * * Imported CTDOntology tree-structure for pruning 24 and 51 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-BioTypes.txt 15 and 14 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-Cardiac_TF_Targets.txt 9 and 8 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-PathwayCommons.txt 0 and 0 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-BioMarkers.txt GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-BioMarkers.sif too large to visualize... Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-microRNATargets.txt 19 and 27 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-MergedTFTargets.txt 7 and 9 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-GO.txt * * * * * * * * * * Imported GeneOntology tree-structure for pruning 102 and 280 edges in the iGraph network. Pruning GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05-local.txt 4 and 3 edges in the iGraph network. gene associations assigned Wikipathways output in 0 seconds Dataset name: GE.42POS_vs_42NEG-downregulated-fold2.0_rawp0.05 130: Reported Filtered GO-terms 53: Reported Elite GO-terms 22: Elite GO-terms redundant with other Elite GO-terms 1: Reported Filtered Pathways 0: Filtered Pathways redundant with other Filtered Pathways 56: Number of genes associated with Filtered GO-terms 49: Number of genes associated with Elite GO-terms 3: Number of genes associated with Filtered Pathways Analysis completed in 300 seconds... Exiting GO-Elite Analysis Complete