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Gene Expression Data Simulator

Contribute a test, normalization/transformation algorithm, classification algorithm!

Number of Differentially Expressed Genes (NR) Start: Stop: Step: Number of Random Genes (R) Number of Iterations Data Distribution Model Uniform Distribution Gamma Distribution Mixed Gamma Distribution Cauchy Distribution Gene Expression Intensity Scale Parameter (β) Upper Bound Gene Expression Intensity Shape Parameter (α) Lower Bound Gene Expression Intensity Scale Parameter (β) 2 Gene Expression Intensity Shape Parameter (α) 2 Background Noise No Yes Background Intensity Scale Parameter (β) Background Intensity Shape Parameter (α) Nonlinear, intensity-related heteroscedascity (group 1 only) No Yes Rocke and Durbin linear scaling constant e1 (bias) Rocke and Durbin nonlinear constant h Heteroscedastic constant k Pattern of Inheritance Jitter Factor 1 (v1) Gene Expression Change Model Post Inheritance Change (PIC) Model NR + R Model Location of Node Separating Groups A and B Change in Upper Magnitude of Differential Expression : ΔXAB Change in Y axis : ΔrAB Start: Stop: Step: Sample Bias Type None Additive Multiplicative Additive + Multiplicative Multiplicative + Additive Random Random Sample Bias Iterations Additive Sample Bias (%SD) Multiplicative Sample Bias Factor

Gene Regulatory Network None Random Network Number of Networks Number of Genes in each Network Gene Regulation Direction Proportion (Up/ Down) Maximum Number of Connection from each Gene Decay Factor

Background Noise Correction None Intensity - Background Intensity - Mean(Sample Background) Intensity - Mean(Dataset Background) Intensity - Median(Sample Background) Hi-Pass Filter (Type-I) Hi-Pass Filter (Type-II) Hi-Pass Filter Var Normalization Step 1 None Handle Negative Numbers ----------------------------------------------------------------------- Filter Negative Numbers Subtract Global Minimum Log Transformation ----------------------------------------------------------------------- Log - Base 2 Log - Base 10 Log - Base e Conditional Log Transform Multiplicative Linear Normalization ----------------------------------------------------------------------- - - - - Within Array - - - Sum Mean Median Quantile Trimmed Mean - - - - Among Array - - - Minimum Mean Ratio Median Mean Ratio Additive Linear Normalization ----------------------------------------------------------------------- - - - - Among Array - - - Global Mean Adjustment Max=1, Min=0 Other Normalization ----------------------------------------------------------------------- Z Transform 5% - 95% Adjustment Two Step Normalization Square Root Transformation Quantile Normalization Order 99 95 90 75 50 25 1 - 99 5 - 95 10 - 90 25 - 75 Global Normalization (Not Recommended) Normalization within samples Normalization within genes (Not Recommended) Normalization within samples + genes (Not Recommended) Normalization within genes + samples (Not Recommended) Normalization within groups (Not Recommended) Normalization Step 2 None Handle Negative Numbers ----------------------------------------------------------------------- Filter Negative Numbers Subtract Global Minimum Log Transformation ----------------------------------------------------------------------- Log - Base 2 Log - Base 10 Log - Base e Conditional Log Transform Multiplicative Linear Normalization ----------------------------------------------------------------------- - - - - Within Array - - - Sum Mean Median Quantile Trimmed Mean - - - - Among Array - - - Minimum Mean Ratio Median Mean Ratio Additive Linear Normalization ----------------------------------------------------------------------- - - - - Among Array - - - Global Mean Adjustment Max=1, Min=0 Other Normalization ----------------------------------------------------------------------- Z Transform 5% - 95% Adjustment Two Step Normalization Square Root Transformation Quantile Normalization Order 99 95 90 75 50 25 1 - 99 5 - 95 10 - 90 25 - 75 Global Normalization (Not Recommended) Normalization within samples Normalization within genes (Not Recommended) Normalization within samples + genes (Not Recommended) Normalization within genes + samples (Not Recommended) Normalization within groups (Not Recommended) Normalization Step 3 None Handle Negative Numbers ----------------------------------------------------------------------- Filter Negative Numbers Subtract Global Minimum Log Transformation ----------------------------------------------------------------------- Log - Base 2 Log - Base 10 Log - Base e Conditional Log Transform Multiplicative Linear Normalization ----------------------------------------------------------------------- - - - - Within Array - - - Sum Mean Median Quantile Trimmed Mean - - - - Among Array - - - Minimum Mean Ratio Median Mean Ratio Additive Linear Normalization ----------------------------------------------------------------------- - - - - Among Array - - - Global Mean Adjustment Max=1, Min=0 Other Normalization ----------------------------------------------------------------------- Z Transform 5% - 95% Adjustment Two Step Normalization Square Root Transformation Quantile Normalization Order 99 95 90 75 50 25 1 - 99 5 - 95 10 - 90 25 - 75 Global Normalization (Not Recommended) Normalization within samples Normalization within genes (Not Recommended) Normalization within samples + genes (Not Recommended) Normalization within genes + samples (Not Recommended) Normalization within groups (Not Recommended) "House Keeping" Genes Correction No Yes "House Keeping" Genes Count Lower Percentile for Housekeeping Genes

Permutation Test No Yes Permutation Count Permutation Threshold Test Criteria Single Test Combined Test Pooled Variance t Test Simple t Test J5 Test n fold [(M1-M2)/M2] Signal to Noise Ratio n fold [Ratio of Mean] n fold [Mean of Ratios] Simple Separability Test Test for Differentially Expressed Genes J5 Test Pooled Variance t Test Simple t Test Simple Separability Test Weighted Separability Test n fold [(M1-M2)/M2] (Not Recommended) n fold [Ratio of Mean] (Not Recommended) n fold [Mean of Ratios] (Not Recommended) D1 Test (Under Development) Signal to Noise Ratio (Furey et. al., 2000) BSS/WSS Ratio (Dudoit et. al., 2002) Threshold Alpha = 1.0 Alpha = 0.1 Alpha = 0.05 Alpha = 0.02 Alpha = 0.01 Alpha = 0.001 Alpha = 1.0 Alpha = 0.1 Alpha = 0.05 Alpha = 0.025 Alpha = 0.01 Alpha = 0.005 Alpha = 0.001 n Fold Ratio Threshold Measure of Central Tendency Mean Median Trimmed Mean Proportion of SD to calculate trimmed mean Special Options None JK to Reduce False Positives MDSS (Lyons-Weiler et.al., 2003) Jackknife Count Minimum Cluster Count Maximum Gene Set Count

Distance Function Euclidean distance 1-Pearson's Correlation (Not Recommended) Manhattan/City block distance (Not Recommended) Chebychev distance (Not Recommended) Canberra distance (Not Recommended) Minkowski Distance (Not Recommended) Clustering Algorithm Average Linkage Clustering Maximum Linkage Clustering Minimum Linkage Clustering K-Mean Clustering Pitt N-Neighbours Clustering Iterations Neighbourhood Size Common Neighbours

Computational Validation Option None External Leave One Out Validation Cross Fold Validation Bootstrap X Fold Iterations Bootstrap Iterations Percentage of Samples in Training Set

Enforce Sample Correlation Yes No                             Group                   Sample 1                                       Sample 2                                     Sample 3                                     Sample 4                                     Sample 5                               Sample 6                                   Sample 7                                     Sample 8                                     Sample 9                               Sample 10                             Sample 11                             Sample 12                                   Sample 13                               Sample 14                                   Sample 15                                     Sample 16   Parent Cell                                         Sample 17                                   Sample 18                                 Sample 19                                 Sample 20                                 Sample 21                           Sample 22                               Sample 23                                 Sample 24                                       Sample 25                                   Sample 26                                 Sample 27                                 Sample 28                                       Sample 29                                   Sample 30                                       Sample 31                                         Sample 32

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