1. EGAN: Exploratory Gene Association Networks by Jesse Paquette Biostatistics and Computational Biology Core Helen Diller Family Comprehensive Cancer Center University of California, San Francisco (AKA BCBC HDFCCC UCSF)

2. EGAN http://akt.ucsf.edu/EGAN/http://akt.ucsf.edu/EGAN/ Features –Downloadable Java application – but could be re-composed as components for web service architecture –Graphics provided by Cytoscape; graph layout algorithms imported from open source –Data pre-loaded for analysis. Each data set must include assay id, a measure (e.g., correlation coefficient, expression level) and significance value (e.g., p value) –Currently for Human and Rat Genome, but other model species in August (including arabidopsis) Key focus- interactive analysis of sets of genes –User identifies the sets interactively –Enrichment -- uses Fishers exact test to see whether genes in a pathway are “overrepresented” relative to chance selection. Based on hypergeometric distribution, an n choose k sampling distribution –Gene sets graphed based on relationships Counts (simply connect each gene to others in the set– can graph multiple sets) Protein-protein interaction Co-occurrence in literature –Access to pub med literature and external links For demos, slides, presentations http://akt.ucsf.edu/EGAN/documentation.php

3. Producing insight from clusters and gene lists Summarize: find enriched pathways (and other gene sets) –Hypergeometric over-representation DAVID –Global trends GSEA Visualize: gene relationships in a graph –Protein-protein interactions Cytoscape –Network module discovery Ingenuity IPA –Literature co-occurrence PubGene Contextualize: pertinent literature PubMed Google iHOP

4. High-throughput experiments EGAN applies to –Expression microarrays –aCGH –SNP/CNV arrays –MS/MS Proteomics –DNA methylation –ChIP-Seq –RNA-Seq –In-silico experiments If parts of the output can be mapped to gene IDs –You can use EGAN

7. Gene sets EGAN contains a database of gene sets –You can also add your own –Download from MSigDB (Broad) A gene set defines a semantically-meaningful subset of genes –Signaling or metabolic pathway –Gene Ontology (GO) term –Previously-reported gene list (“signature”) –Cytoband –Transcription factor targets –miRNA targets –Conserved domain –Drug targets –&c.

10. Gene-gene relationships EGAN contains –Protein-protein interactions (PPI) –Literature co-occurrence –Chromosomal adjacency –Kinase-target relationships

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14. Finding Counts

17. EGAN Summary: Exploratory Gene Association Networks Methods: state-of-the-art analysis of clusters and gene lists –Hypergeometric enrichment of gene sets –Global trends of gene sets –Graph visualization –Literature identification –Network module discovery User Interface: responds quickly to new queries from the biologist –Fluid adjustment of p-value cutoffs –Point-and-click interface –All data in-memory for immediate access –Links to external websites Modular: integrates as a flexible plug-and-play cog –All data is customizable –Proprietary data can be restricted to the client location –Java runs on almost every OS (PC, Mac, LINUX) –Can be configured and launched from a different application (e.g. GenePattern) –Analyses can be scripted for automation

18. Keys to getting the most out of EGAN Don’t panic! Load as much data as possible –Assay results for every gene –Multiple experiments –Pathways and gene sets MSigDB –Previously-published gene lists and clusters Supplementary data Oncomine Think about the context of the experiment –Show appropriate genes on graph Think about the semantic meaning of the enriched gene sets –Show appropriate gene sets on graph Follow links to literature Use appropriate Google/PubMed search queries Create high-quality reports –Save your custom gene sets –Export graph screenshots to PDF –Export tables with enrichment scores to Excel –Record details in your lab notebook

19. Where to find EGAN Website –http://akt.ucsf.edu/EGAN/http://akt.ucsf.edu/EGAN/ 2010 paper in Bioinformatics –http://www.ncbi.nlm.nih.gov/pubmed/19933825http://www.ncbi.nlm.nih.gov/pubmed/19933825