Gnc march 2012
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  • 1. Gene Network Central (GNC) Pro Webinar An Online in silico Tool to Explore the Biology Around Your Genes of Interest George J. Quellhorst, Jr, Ph.D. Associate Director R&D Bioinformatics – Biological Content Development Wednesday, March 14, 2012 -1- Sample & Assay Technologies
  • 2. What is Gene Network Central Pro? • Pathway Analysis / Systems Biology Software • Integrates Multiple Bioinformatic Resources • Information Authority for Life Sciences Research • Takes Advantage of Our Pathway Expertise -2- Sample & Assay Technologies
  • 3. What Can GNC Pro Do for You? • Analyze PCR Array Data & Develop Follow-Up Experiments • How do differentially regulated genes have in common? • Choose the Right Product for Your Research • Are these genes actually expressed in my model system? • Collect genes for a Custom PCR Array • Find model system to analyze gene function (by RNAi) • Why are these genes in this pathway? • Expedite your research process • Share data through exported graphical or textual formats • Simple & easy to access, understand & use -3- Sample & Assay Technologies
  • 4. “Canonical” Pathway Versus Gene Network Example: Notch Signaling Pathway Canonical Gene Network Cellular Context Provided Misses Other Related Genes Includes Other Interacting Genes From Cross-Talking Pathways -4- Sample & Assay Technologies
  • 5. Network Graph Theory 101 Definitions: • Graph: Pictorial device visually illustrating relationships • Network: Complex, interconnected group or system • Node: Vertex; end point for interactions and data transmissions in a graph • Edges: Links & relationships between nodes (vertices) Edges Nodes Network Graph -5- Sample & Assay Technologies
  • 6. GNC Pro Graphical Network Implementation • • Nodes = Genes / Proteins Different Shapes & Colors = Different Annotations (Input & Neighbors) • Edges = Relationships between Genes / Proteins each with different attributes: • Color = Relationship Type • Physical Interaction • Functional / Transcriptional Regulation • Post-Translational Modification • Co-Expression • Solid = Discovered; Dashed = Predicted • Arrowheads = Directionality (if applicable) • Opacity ~ Relationship Strength / Certainty -6- Sample & Assay Technologies
  • 7. GNC Pro Computational Implementation Three-Tier Structure: Back end Front end • • Web Browser Graphical User Interface (GUI) Web Server -7- Database Server Sample & Assay Technologies
  • 8. GNC Pro Graphical User Interface Front End: • Web-Based, Graphical User Interface • Quickly find neighboring genes that associate with your genes of interest • Easily visualize different types of interactions • Access supporting data for the interactions • View genes and networks within the context of tissues • Freely manipulate graph through interactive controls -8- Sample & Assay Technologies
  • 9. GNC Pro Knowledge Base Data Sources Back End: • Multiple data sources seamlessly integrated into a single platform • Systematic Quality Control by Biological Scientists • Powerful text-mining algorithm & database processing biomedical publications with high accuracy and sensitivity • Gene A – Verb – Gene B • Public & Licensed resources data mined for omics data • Nature / NCI Pathway Interaction Database, Gemma, ProLinks • HPRD Textmining • Tissue-Specific Gene Expression Datamining • BioGPS (GNF), U Tokyo, HUGE • Pre-Loaded Pathways Calculations/Predictions • Nature / NCI PID • KEGG, Reactome • PCR Arrays • Gene Ontology -9- Sample & Assay Technologies
  • 10. GNC Pro Knowledge Base Source Unique Unique Total Genes Relationships Relationships Text-Mined Data 6,384 36,283 97,795 Data-Mined Chemical Modifications 1,291 2,354 2,354 Third Party Protein Interactions 8,433 32,805 32,805 Data-Mined Co-Expression Data 8,526 216,104 216,267 Protein-Protein Interaction Predictions 8,152 43,364 43,364 Transcription Factor Regulation Predictions 13,684 122,700 122,700 TOTAL 20,116 448,255 515,285 - 10 - Sample & Assay Technologies
  • 11. Gene Network Central Pro Live Demo http://gncpro.sabiosciences.com http://www.sabiosciences.com - 11 - Sample & Assay Technologies
  • 12. GNC Pro: Feature Highlights Interactively Explore the Network: • Expand graph and “walk” the network • Move nodes around via drag-and-drop or delete unwanted nodes • Reorganize or restore original graph via controls Manipulate Network Appearance via Simple Controls: • Association types • Functional Regulation: positive/negative regulation of gene products • Transcriptional Regulation: regulation of gene expression • Chemical Modification: post-translational modification • Physical Interaction: physical association or co-localization relations • Co-Expression: negative/positive correlation of gene expression - 12 - Sample & Assay Technologies
  • 13. GNC Pro: Handy Access to Rich Resources View Information Within Tissue-Specific Context: • Simple drop-down box to apply tissue overlays to graph data • View tissue-expression profile information for a single gene Quickly Accessible & Useful Links: • Clickable associations link out to supporting websites and documentation • Clickable genes link out to pages with more, gene-specific information • Simple links at the right allow easy access to related research products with in-depth information to guide you to the right solution - 13 - Sample & Assay Technologies
  • 14. GNC Pro: An Evolving Tool - 14 - Sample & Assay Technologies
  • 15. Questions? Ask now or contact Technical Support M – F, 9 AM – 6 PM Eastern Telephone: (888) 503-3187 OR Email: support@SABiosciences.com - 15 - Sample & Assay Technologies
  • 16. Gene Network Central (GNC) PRO Webinar An Online in silico Tool to Explore Biological Systems Around Your Genes of Interest George J. Quellhorst, Jr, Ph.D. Associate Director R&D Bioinformatics – Biological Content Development Wednesday, November 30, 2011 - 16 - Sample & Assay Technologies