1. GenePattern Overview for MAGE-TAB Workshop Ted Liefeld January 24, 2007

2. a platform for integrative genomics Client User Interfaces Pipeline Environment Module Repository Module Integrator Desktop Programming Web all_aml_train all_aml_test Preprocess Class Neighbors Weighted Voting Cross-Val SOM Clustering Preprocess Weighted Voting Train/Test SOM Cluster Viewer Marker Selection Viewer Prediction Results Viewer Prediction Results Viewer Golub and Slonim et. al 1999 KNN SVM SOM GSEA NMF PCA

6. Statistical Methods & Machine Learning Analyses Prediction K-Nearest Neighbors (KNN) Weighted Voting (WV) Support Vector Machines (SVM) Probabilistic Neural Networks (PNN) Classification and Regression Trees (CART) Clustering Hierarchical k-Means SOM Consensus Pathway Analysis GSEA ARACNE Cytoscape Other Statistical Methods Missing value imputation Kolmogorov-Smirnov score Non-negative Matrix Factorization (NMF) Principal Components Analysis (PCA)

9. as a Visualization & Analysis Engine http://www.broad.mit.edu/mmgp Portal GenePattern GenePattern SNPViewer visualizer (running as applet) Run GenePattern Analyses LSF Worker Nodes

10. Using MAGE-ML today