interpret gene expression results 2013
TRANSCRIPT
Sample & Assay Technologies
Biologically Interpret Gene Expression Analyses George J. Quellhorst, Jr. Ph.D. Associate Director, R&D – Biological Content Development
Sample & Assay Technologies Agenda
� Introduction� Analyzing Gene Expression Results
� Getting Started� Walk Around the Network
– Knowledgebase� Quality Assurance & Quality Control� Final Steps� Use Case Scenario Demonstrations
� Summary & Discussion� Q & A
What Will We Discuss?
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Sample & Assay Technologies Introduction
� Pathway Analysis / Systems Biology Software� Integrates Multiple Bioinformatics Resources
� Information Authority for Life Sciences Research� Takes Advantage of Our Pathway Expertise
� Expedite your research process� Share data through exported graphs & texts� Simple & easy to access, understand & use
� Choose the Right Product for Your Research� Custom PCR Arrays – Another Webinar
– Expand seed gene list using interactome data� Analyze PCR Array Data - TODAY
� Develop Follow-Up Experiments
What is GNC Pro?
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Sample & Assay Technologies Analyzing Gene Expression Results
� RT2 Profiler PCR Array Data Analysis Web Portal� What’s Next OR Export Data
– Significantly differentially expressed genes� Change to “Up” or “Down”
� Input Gene List� Cut-and-paste� Upload text file� Select Two Columns
Getting Started
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Sample & Assay Technologies Analyzing Gene Expression Results
� How genes interact with one another� Expand Graph� Get More Neighbors
� Other genes interacting with inputted genes� Either entire set or one gene at a time
� Gene Centered Network� Focus on just one gene� See just what interacts with it
Walk Around the Network
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Sample & Assay Technologies Knowledgebase Interactome Sources
� Multiple Data Sources – One Platform� Systematic Quality Control by Biological Scientists� Powerful Text-Mining Algorithm & Database
� Processes biomedical publications� Gene A – Verb – Gene B� High accuracy & sensitivity
� Public & Licensed Omics Resources Datamined� Nature / NCI Pathway Interaction Database� Gemma� ProLinks� HPRD
� Tissue-Specific Gene Expression� BioGPS (GNF), U Tokyo, HUGE
Where are these new genes coming from?
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Datamining
Textmining
Calculations/Predictions
Sample & Assay Technologies Knowledgebase Depth
SourceUniqueGenes
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
How Many & What Kinds of Interactions?
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Sample & Assay Technologies Analyzing Gene Expression Results
� Verify Interactions� Click lines connecting genes
– Displays evidence for relationship� Not convinced?
– Delete Gene to remove individual genes– Helps narrow down longer gene lists
� Are Genes Expressed in Your Model System?� View Tissue Specific Expression
– One gene at a time or entire network
Quality Assurance & Quality Control
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Sample & Assay Technologies Analyzing Gene Expression Results
� Export Graph Image� JPG or PNG� Opens new window with image� Save using internet browser “Save Graph” function
� Export Genes� Opens Excel file with gene list and all interactions
� Find Related Products� Search for the right gene-specific assay for your next
experiment– shRNA Plasmids– Real-Time RT-PCR Assays
Final Steps
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Sample & Assay Technologies Use Case Scenario Demonstrations
� Stimulate Human PMBCs with Phorbol Ester & Ionomycin for six & 24 hours� Characterize RNA on Human Common Cytokines RT2 Profiler PCR Array� Same experiment used in PCR Array Data Analysis webinar
Let’s see this in action with real data
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Sample & Assay Technologies Summary & Conclusions
� Start� Organize & Input Gene List
� Walk Around� Expand Graph & Get More Neighbors
� Verify� Evidence for Interactions� Tissue Specific Expression
� Finalize� Export Genes & Interactions� Order Assays for Next Experiment
Analyze Your PCR Array Data Today
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Sample & Assay Technologies Summary & Discussion
� Canonical Pathways� Pathway Central Maps� Cellular Context� Network Pathways will still be available
� Genes Color Coded by Fold Change� In both canonical & network pathway views
Coming Soon
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Sample & Assay Technologies Questions?
GNC Pro Related Questions: Ask Now OR Email Technical Support at [email protected]
Webinar Related Questions: Email [email protected]� Saved PDF Slides & Recorded Sessions� Alternative Times� New Topics You Want to See
Resources to Further Help You
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Sample & Assay Technologies
Biologically Interpret Gene Expression Analyses George J. Quellhorst, Jr. Ph.D. Associate Director, R&D – Biological Content Development