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Gene Network Central (GNC) Pro Webinar
George J. Quellhorst, Jr, Ph.D.Associate Director R&D
Bioinformatics – Biological Content Development
Wednesday, March 14, 2012
An Online in silico Tool to Explore the BiologyAround Your Genes of Interest
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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
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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
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“Canonical” Pathway Versus Gene Network
Example: Notch Signaling Pathway
Cellular Context ProvidedMisses Other Related Genes
Canonical Gene Network
Includes Other Interacting GenesFrom Cross-Talking Pathways
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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)
Nodes
Network Graph
Edges
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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
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GNC Pro Computational Implementation
Three-Tier Structure:
• Web Browser• Graphical User Interface
(GUI)
Front end
Web ServerDatabase Server
Back end
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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
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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
• Tissue-Specific Gene Expression• BioGPS (GNF), U Tokyo, HUGE
• Pre-Loaded Pathways• Nature / NCI PID• KEGG, Reactome• PCR Arrays• Gene Ontology
Datamining
Textmining
Calculations/Predictions
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GNC Pro Knowledge Base
Source UniqueGenes
UniqueRelationships
TotalRelationships
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
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Gene Network Central Pro Live Demo
http://gncpro.sabiosciences.com
http://www.sabiosciences.com
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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
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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
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GNC Pro: An Evolving Tool
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Questions?
Ask now or contact Technical Support M – F, 9 AM – 6 PM Eastern
Telephone: (888) 503-3187 OR Email: [email protected]
Sample & Assay Technologies- 16 -
Gene Network Central (GNC) PRO Webinar
George J. Quellhorst, Jr, Ph.D.Associate Director R&D
Bioinformatics – Biological Content Development
Wednesday, November 30, 2011
An Online in silico Tool to Explore Biological Systems Around Your Genes of Interest