SUPPLEMENTAL FIGURES AND TABLES

1. SUPPLEMENTAL FIGURES AND TABLES

2. Legends for Supplementary Figures & Table 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.

3. 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