#Main Input: Data_File Gene_Annotation_Source User provided Gene_Annotation_File Cross_Reference_Source User provided Cross_Reference_File Clustering_Method[STEM Clustering Method,K-means] STEM Clustering Method Maximum_Number_of_Model_Profiles 50 Maximum_Unit_Change_in_Model_Profiles_between_Time_Points 2 Number_of_Clusters_K 10 Number_of_Random_Starts 20 Normalize_Data[Log normalize data,Normalize data,No normalization/add 0] Normalize data Spot_IDs_included_in_the_data_file false #Repeat Data: Repeat_Data_Files(comma delimited list) Repeat_Data_is_from[Different time periods,The same time period] Different time periods #Comparison Data: Comparison_Data_File Comparison_Maximum_Uncorrected_Intersection_pvalue .005 Comparison_Minimum_Number_of_genes_in_intersection 5 Comparison_Repeat_Data_Files(comma delimited list) Comparison_Repeat_Data_is_from[Different time periods,The same time period] Different time periods #Filtering: Maximum_Number_of_Missing_Values 0 Minimum_Correlation_between_Repeats 0 Minimum_Absolute_Log_Ratio_Expression 1 Change_should_be_based_on[Maximum-Minimum,Difference From 0] Maximum-Minimum Pre-filtered_Gene_File #Model Profiles: Maximum_Correlation 1 Number_of_Permutations_per_Gene 50 Maximum_Number_of_Candidate_Model_Profiles 1000000 Significance_Level .05 Correction_Method[Bonferroni,False Discovery Rate,none] Bonferroni Permutation_Test_Should_Permute_Time_Point_0 true #Clustering: Clustering_Minimum_Correlation 0.7 Clustering_Minimum_Correlation_Percentile 0 #Gene Annotations: Category_ID_file Include_Biological_Process true Include_Molecular_Function true Include_Cellular_Process true Only_include_annotations_with_these_evidence_codes Only_include_annotations_with_these_taxon_IDs #GO Analysis: Minimum_GO_level 3 GO_Minimum_number_of_genes 5 Number_of_samples_for_randomized_multiple_hypothesis_correction 500 Multiple_hypothesis_correction_method_enrichment[Bonferroni,Randomization] Randomization #Interface Options Gene_display_policy_on_main_interface[Do not display,Display only selected,Display all] Do not display Gene_Color(R,G,B) 204,51,0 Y-axis_scale_for_genes_on_main_interface_should_be[Gene specific,Profile specific,Global] Profile specific Y-axis_scale_for_genes_on_k-means_main_interface_should_be[Cluster specific,Global] Global Scale_should_be_based_on_only_selected_genes true Y-axis_scale_on_details_windows_should_be[Determined automatically,Fixed] Determined automatically Y_scale_min -3 Y_scale_max 3 Tick_interval 1 X-axis_scale_should_be[Uniform,Based on real time] Uniform