1. SUPPLEMENTAL FIGURES AND TABLES

2. Supplementary Table 1: List of new and improved features in GSEA-P version 2 Java software. Examples and screenshots can be found at: http://www.broad.mit.edu/GSEA/doc/whats_new. Supplementary Figure 1: The ‘Run GSEA’ panel that allows datasets to be collapsed from a number of microarray platforms into Entrez gene symbols. Supplementary Figure 2: GSEA-P plot (in green) of the running enrichment score of the RAS pathway in a comparison of expression profiles from P53 mutant vs. wild type cell lines. The black bars in the center section indicate locations of the RAS pathway members in the list of genes ranked by their differential expression. The red-blue color bar is a heat map of the correlation of genes with the P53 mutant vs. wild type phenotype, while the plot in gray is the graph of correlation value with respect to position in the gene list. Supplementary Figure 3: (A) Leading edge plot of the top 10 enriched gene sets from a comparison of P53 wild type vs. mutant expression profiles. Genes in red are present in several of the gene sets upregulated in the mutant class and genes in blue are upregulated in the wild type class. (B) Jacquard matrix of the overlap between the top 10 gene sets. Supplementary Figure 4: (A) The Chip2Chip panel that provides a tool to map identifiers between platforms. (B) Currently, GSEA-P 2.0 supports mappings for 93 platforms. Supplementary Figure 5: The MSigDB browser showing a list of gene sets alongside several search options. Supplementary Figure 6: The MSigDB web page showing the 4 gene set collections. Supplementary Figure 7: Screenshot of a single GeneSetCard. These are web pages with annotations including the source and biological relevance of MSigDB gene sets. Legends for Supplementary Figures & Table

3. COMPONENTNEW ( # ) AND IMPROVED (*) FEATURES IN GSEA-P VERSION 2 Running GSEADataset collapsing (conversion of native probe ids to gene symbols) available directly in the GSEA panel as an option Enrichment reports If the gene set is from MSigDB, a hyperlink to the Gene Set Card is automatically inserted in the report # Custom gene sets can gain similar annotation by inserting an http:// value in the gene set matrix file # Snapshot page gives a global picture of the top 20 (or as specified) enriched gene sets # Enrichment mountain plot includes a color bar that depicts the phenotype correlation (e.g signal-to-noise scores)* Gene marker permutation report for easy comparison b/w genes and gene sets # Chip platform annotations Several new microarray platforms added (total is now 93)* Custom chip annotations can be specified by adding a.chip file to the gsea_home/anotations folder* Chip2ChipGene sets can be converted between gene symbols  93 chip platforms # Gene sets can be converted between chip platforms # Addition of a gene thesarus for mapping gene sets into standard HUGO gene symbols. Alias database for gene symbols from Unigene (release 180) and internally curated # SystemThe application base directory (gsea_home) can be installed anywhere on the file system and its location specified by a preference setting* Object browser displays datasets currently in memory # Batch modeCommand line usage simplified by adding defaults for algorithm parameters* Heat maps and all other visualizations will be made even in headless mode* Gene set cardsHTML page containing extensive annotation about the derivation of a gene set including source, category and PubMedID (when available) # Gene set browser Browse gene sets in MSigDB from within the GSEA-P software # Search for gene sets in several ways including by gene and by abstract keyword # DocumentationComprehensive user manual # Software tutorial* FAQ* Wiki # Supplementary Table 1: List of new and improved features in GSEA-P version 2

4. Supplementary Figure 1: Run GSEA panel

5. Supplementary Figure 2: GSEA-P plot (in green) of the running enrichment score of the RAS pathway

6. Supplementary Figure 3A & 3B: Leading edge analysis

7. Supplementary Figure 4A: Chip2Chip: map gene sets between platforms

8. Supplementary Figure 4B: Platform annotations available via FTP

9. Supplementary Figure 5: MSigDB gene sets browser

10. Supplementary Figure 6: New MSigDB release

11. Supplementary Figure 7: Gene Set Cards