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DREM_defaults.txt
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#Main Input:
TF-gene_Interaction_Source User Provided
TF-gene_Interactions_File
Expression_Data_File ../../human/egf/Yarden_MCF10A_expr.txt
Saved_Model_File
Gene_Annotation_Source No annotations
Gene_Annotation_File
Cross_Reference_Source User Provided
Cross_Reference_File
Normalize_Data[Log normalize data,Normalize data,No normalization/add 0] Log normalize data
Spot_IDs_in_the_data_file false
#Repeat Data:
Repeat_Data_Files(comma delimited list)
Repeat_Data_is_from[Different time periods,The same time period] The same time period
#Filtering:
Filter_Gene_If_It_Has_No_Static_Input_Data false
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] Difference From 0
Pre-filtered_Gene_File
#Search Options
Allow_Path_Merges false
Maximum_number_of_paths_out_of_split 2
Use_transcription_factor-gene_interaction_data_to_build true
Saved_Model[Use As Is/Start Search From/Do Not Use] Use As Is
Convergence_Likelihood_% 0.01
#Model Selection Options
Model_Selection_Framework[Penalized Likelihood,Train-Test] Penalized Likelihood
Penalized_Likelihood_Node_Penalty 40
Random_Seed 1260
Main_search_score_% 0
Main_search_difference_threshold 0
Delete_path_score_% 0.15
Delete_path_difference_threshold 0
Delay_split_score_% 0.15
Delay_split_difference_threshold 0
Merge_path_score_% 0.15
Merge_path_difference_threshold 0
#Gene Annotations:
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
Category_ID_file
#GO Analysis
Minimum_GO_level 3
Minimum_number_of_genes 5
Number_of_samples_for_randomized_multiple_hypothesis_correction 500
Multiple_hypothesis_correction_method_enrichment[Bonferroni,Randomization] Randomization
#Interface
X-axis_Scale_Factor 1
Y-axis_Scale_Factor 1
X-axis_scale[Uniform,Based on Real Time] Based on Real Time
Key_Input_X_p-val_10^-X 3
Minimum_Split_Percent 0
Scale_Node_Areas_By_The_Factor 1
Key_Input_Significance_Based_On[Path Significance Conditional on Split,Path Significance Overall,Split Significance] Path Significance Conditional on Split
#SDREM
Active_TF_influence 0.8