Interpret gene expression results 2013

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Interpret gene expression results 2013

  1. 1. Sample & Assay Technologies Biologically Interpret Gene Expression Analyses George J. Quellhorst, Jr. Ph.D. Associate Director, R&D – Biological Content Development
  2. 2. Sample & Assay Technologies Agenda What Will We Discuss? 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 2
  3. 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 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 3
  4. 4. Sample & Assay Technologies Analyzing Gene Expression Results Getting Started 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 4
  5. 5. Sample & Assay Technologies Analyzing Gene Expression Results Walk Around the Network 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 5
  6. 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 6
  7. 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 7
  8. 8. Sample & Assay Technologies Analyzing Gene Expression Results Quality Assurance & Quality Control 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 8
  9. 9. Sample & Assay Technologies Analyzing Gene Expression Results Final Steps 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 9
  10. 10. Sample & Assay Technologies Use Case Scenario Demonstrations Let’s see this in action with real data 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 10
  11. 11. Sample & Assay Technologies Summary & Conclusions Analyze Your PCR Array Data Today 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 11
  12. 12. Sample & Assay Technologies Summary & Discussion Coming Soon 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 12
  13. 13. 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 Biologically Interpret Gene Expression Analyses, Webinar, Tuesday, March 12, 2013 13
  14. 14. Sample & Assay Technologies Biologically Interpret Gene Expression Analyses George J. Quellhorst, Jr. Ph.D. Associate Director, R&D – Biological Content Development

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