1. Sample & Assay Technologies
Build Your Own Gene Expression Analysis Panels
George J. Quellhorst, Jr. Ph.D.
Associate Director, R&D

2. Sample & Assay Technologies
Agenda
What Will We Discuss?
Introduction
Building Your Own Gene List
Getting Started
Increasing Coverage
Knowledgebase Interactome Sources
– Where are these new genes coming from?
– How many & what kinds of interactions?
Quality Assurance & Quality Control
Final Steps
Use Case Scenario Demonstrations
Summary & Discussion
Q&A
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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3. Sample & Assay Technologies
Introduction
What is GNC Pro?
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
Analyze PCR Array Data – Upcoming Webinar
Develop Follow-Up Experiments
Choose the Right Product for Your Research
Cataloged & Custom PCR Arrays
– Expand seed gene list using interactome data
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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4. Sample & Assay Technologies
Building Your Own Gene List
Getting Started
Check with PCR Array Pathways First
“Off-the-Shelf” Arrays Catalog
Is there a title matching the biology you study?
Start with a “Seed” Gene List Source:
Your Own Short Gene List
Pre-Loaded Pathways:
– Cancer Pathways (Nature/NCI, > 500)
– Signaling, Metabolic & General Pathways (KEGG & Reactome, > 200)
– Genes Associated with Human Diseases (OMIM, > 4000)
– Gene Ontologies (1000s)
Search each one systematically
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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5. Sample & Assay Technologies
Building Your Own Gene List
Increasing Coverage
Some gene lists long enough – skip to next step
Some gene lists short – more genes likely involved
More genes related to “seed” gene list
Expand Graph
– Finds new genes with relationships to as many
inputted genes as possible
Get More Neighbors
– Finds new genes with relationships to single
selected gene
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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6. Sample & Assay Technologies
Knowledgebase Interactome Sources
Where are these new genes coming from?
Datamining
Textmining
Calculations/Predictions
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
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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7. Sample & Assay Technologies
Knowledgebase Depth
How Many & What Kinds of Interactions?
Unique
Genes
Source
Unique
Relationships
Total
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
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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8. Sample & Assay Technologies
Building Your Own Gene List
Quality Assurance & Quality Control – Final Steps
Verify Interactions
Click lines connecting genes
– Displays evidence for relationship
Not convinced?
– Delete Gene remove individual genes
– Helps narrow down longer gene lists
Are Genes Expressed in Your Model System?
View Tissue Specific Expression
Export Genes
Ready for submission as a Custom Gene List
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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9. Sample & Assay Technologies
Use Case Scenario Demonstrations
Let’s see this in action
Human Diseases
Schizophrenia
Polycystic Kidney Disease
Metastatic Melanoma
Glaucoma
Cancer Pathways
Complement
Calmodulin
General Pathways
Rho GTPases
Gene Ontologies
AMPK Signaling
Your Biology of Interest
Type your ideas into “Questions” box – Webinar right-hand navigation bar
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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10. Sample & Assay Technologies
Summary & Conclusions
Build Your Own Gene List Today OR Let Us Help
Start
Biological Search Term OR Short Gene List
Expand
Expand Graph & Get More Neighbors
Verify
Evidence for Interactions, Tissue Specific Expression
Finalize
Export Genes & Order
Custom Content Generation Services
FREE with purchase of Custom PCR Array
Expert Biological Content Development Scientists
Use This Process & Other Sophisticated Resources
Your Biology -> Best Possible Gene List
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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11. Sample & Assay Technologies
Questions?
Resources to Further Help You
GNC Pro Related Questions:
Ask Now
OR
Email Technical Support at
support@SABiosciences.com
Webinar Related Questions:
Email QIAWEBINARS@QIAGEN.COM
Saved PDF Slides & Recorded Sessions
Alternative Times
New Topics You Want to See
Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012
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12. Sample & Assay Technologies
Build Your Own Gene Expression Analysis Panels
George J. Quellhorst, Jr. Ph.D.
Associate Director, R&D