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Introduction to Oncomine

Introduction to Oncomine. Xiayu Stacy Huang. What is Oncomine?. Oncomine is a cancer-specific microarray database and has a web-based data-mining platform aimed at facilitating discovery from genome-wide expression analysis

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Introduction to Oncomine

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  1. Introduction to Oncomine Xiayu Stacy Huang

  2. What is Oncomine? • Oncomine is a cancer-specific microarray database and has a web-based data-mining platform aimed at facilitating discovery from genome-wide expression analysis • Oncomine was originally developed as an academic tool at the University of Michigan in 2003 and then became a commercial tool in 2006 (Compendia Bioscience). • Oncomine is the world’s largest existing human cancer genomic database that covers 674 independent datasets and more than 73,000 samples.

  3. Oncomine Platform User Interface

  4. What can Oncomine do? • Differential gene expression: What genes are over- or under- expressed in particular cancer types or subtypes? • Co-expression:Is my target gene coordinately expressed with other genes that are members of a biological pathway activated in a cancer type? • Outlier analysis: What genes might be good biomarkers for cancer subtypes? • Comparing (meta-analysis):What gene expression patterns or gene sets are validated across multiple datasets? • Concept list: Can patient subtypes be associated with this signature or gene list representing underlying biology?

  5. Oncomine Editions • Free research edition including • Gene expression and DNA copy number data from clinical and cell-line experiments • Lists of DEGs across multiple experiments • Single gene search (differential expression, co-expression, etc) • Premium research edition including additional features • Multi-gene search • Expanded analysis types including cancer subtypes, drug sensitivity, clinical outcome analysis, etc. • Export and share results, upload custom concepts, and access commercial-level support

  6. How to start? • Requirements • Internet access • Internet explorer 6.0 or higher, firefox • Java script must be enabled • Oncomine login (https://www.oncomine.org) • Example questions: • EGFR over-expression in brain cancer? • any genes that are coexpressed with EGFR? • EGFR expression pattern consistent across multiple studies?

  7. Starting analysis by using search and setting filters Search box Compendia ontology

  8. Determining if EGFR is over-expressed in brain cancer

  9. Meta analysis of EGFR across studies

  10. Finding co-expressed genes with EGFR in brain cancer

  11. Conclusion • By looking at brain and CNS cancer vs. normal analyses, we can conclude EGFR is over-expressed in several independent datasets • By doing meta-analysis, we can conclude the expression pattern of EGFR is quite consistent across multiple independent studies • By doing coexpression analysis, we can conclude there are some genes that are coexpressed with EGFR and further investigation of these coexpressed genes may be needed

  12. Thanks! Any Questions?

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