MetaMiner™ Prostate Cancer
Overview
MetaMiner™ Prostate Cancer (MMPC) represents a version of GeneGo’s MetaDiscovery platform with reconstructed content specific for the disease. MMPC is an ongoing project initiated in 2008 by GeneGo Inc. in collaboration with a major pharmaceutical company to create a committee of expert scientists that also dictate the content with continuous quarterly updates. This iterative process allows GeneGo developers to maintain the specificity of the content and pathways.
In addition to specific content, the MMPC platform extends the application of the MetaDiscovery platforms to include pre-built canonical pathway maps and networks specific for this disease. Therefore, MMPC is a data analysis platform designed to be used by a broad range of prostate cancer researchers including wet lab biologists, bioinformaticians, toxicologists, biomarker researchers, clinicians and chemists.
The current version of MMPC includes the following:
- A one-stop shop “Disease Detail” page summarizing all MMPC information
- 1330 disease-relevant genes
- 211,962 physical and functional interactions with other human proteins, DNA, RNA and compound species.
- prostate cancer-specific gene aberrations and alterations including:
- DNA amplifications
- SNPs and haplotypes
- Epigenetic modifications
- Alternative transcripts
- Transcription level alterations
- Native protein abundance change
- Fusion proteins (the independent role of the fusion protein as well as the individual proteins ie ERG alone, vs TMPRSSE vs their fusion protein)
- Protein isoforms
- Mutant proteins
- Peptide-PC association
- Phosphorylation and other type PTM
- 13 small molecule compounds (endogenous metabolites) associated with the disease
- 241 drugs (with 157 drug targets) including
- 198 small molecules
- 43 biologics
- 26 Prostate cancer-specific canonical GeneGo Maps that include:
- The role of miRNA
- 2 maps with the role of fusion proteins
- Survival pathways
- Over 10 maps that describe the role of key hormones, transcription factors, cytokines, enzymes
- Over 10 maps describing general scheme of underlying biological processes form angiogenesis to EMT, immune response, cell cycle and neuroendocrine transdifferentiation, stromal-epithelial interaction in Prostate Cancer
- 28 datasets from GEO (http://www.ncbi.nlm.nih.gov/geo/) and the Broad Institute at MIT have been annotated, uploaded and normalized including:
- 24 microarray and SAGE profiles
- 3 microRNA profiles
- 1 High copy and variation profile
The advanced applications of MMPC also include integration of GeneGo-based analyses with third-party software suites to enable seamless export of networks or analysis lists from MMPC to Cytoscape, GeneSpring, DecisionSite, ArrayStudio and Resolver, following the addition of the appropriate plug-ins.
Additional Translational Applications of MMPC
- Access to drug details from a search or from a gene/protein/disease of interest
- Biomarker targeting workflows
- Toxicity analysis workflows
- Customization of visual outputs using MetaLink to map novel interactions (unknown to the public domain)
- Customization of visual outputs using MapEditor to create maps with custom objects, text, links and cellular localizations - ideal for hypotheses generation testing and communicating ideas to colleagues
A sample of how MMPC information can be used with GeneGo.s MetaDiscovery platform, down load the following white papers here.
For a training session on how to execute these approaches, please contact training@genego.com.
How to Access the MMPC Platform
Access to the PC maps, networks and disease pages can be obtained using the MetaMiner Prostate Cancer platform that can be licensed from GeneGo Inc. Contact sales@genego.com, Tel: 858 756 7996, for more information and pricing.
