Gnc march 2012

Sample & Assay Technologies- 1 -

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


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


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


“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


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


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


GNC Pro Computational Implementation

Three-Tier Structure:

• Web Browser• Graphical User Interface

(GUI)

Front end

Web ServerDatabase Server

Back end


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


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


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


Gene Network Central Pro Live Demo

http://gncpro.sabiosciences.com

http://www.sabiosciences.com


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


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


GNC Pro: An Evolving Tool


Questions?

Ask now or contact Technical Support M – F, 9 AM – 6 PM Eastern

Telephone: (888) 503-3187 OR Email: [email protected]


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

Gnc march 2012

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