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Pathway studio into webinar 052715v1

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Pathway studio into webinar 052715v1

  1. 1. An introduction to Pathway Studio Helping researchers understand the biology of disease… Frank White, PhD May 27, 2015
  2. 2. | 2 Pathway Studio addresses key challenges across the R&D value chain DISCOVERY PRE- CLINICAL CLINICAL POST- LAUNCH Product Name Mapping to R&D Phase Description Pathway Studio Discovery Target Discovery, Biomarker Discovery, Drug Repurposing, Biological Pathways, Gene Expression, Genomics, Proteomics, Basic Research Preclinical Proteomics, Metabolomics Translational / Clinical Patient Stratification R&D Value Chain
  3. 3. | 3 Pathway Studio overview: Data, tools, visualization Pathway Studio ToolsKnowledgebase Manually curated pathways Ontologies Biological relations extracted from literature Experiment analysis: Gene expression Proteomics Metabolomics NGS data Search Summarization Navigation Visualization 24M abstracts 3.5M full texts 4.8M relations +836K new relations
  4. 4. | 4 Pathway Studio databases cover wide ranging information standard name standard link standard name Mammal protein-centered ChemEffect drug-centered DiseaseFX biomarker-centered +Biomarker facts +Drugs Proteins + • diseases • clinical parameters • small molecules • cell processes • treatments • genetic change • state change • quantitative change Cells* cell-centered +Cell facts Cells
  5. 5. | 5 Benefits: Visualize and understand disease biology • Pathway diagrams provide a view of complex biological processes. • Pathway views provide the context for analyzing neighboring molecules of a particular target. • Drugs may work on a neighboring molecule in the pathway instead of the intended target, so understanding relationships is critical
  6. 6. How can Pathway Studio help you?
  7. 7. | 7 The benefits of more content… • Pathway Studio has 3-5x more literature-derived content than any other resource, so…  No matter what disease you study, you’ll find 2-3 times more connections and pathway members than any other resource… if they have any results at all!  You’ll find more references supporting those relationships, so you’ll have higher confidence in the meaning of your experimental results  You’ll feel more confident about what’s reported in the literature, with more independent references to help you verify reported experimental results
  8. 8. | 8 Start with expertly-curated pathways… Pathway Studio includes almost 1500 expertly- curated reference pathways that you can search, edit, and use to interpret your experimental data. And new pathways are added regularly…
  9. 9. | 9 Focus on what’s important to you… Users can customize how they interact with data in Pathway Studio – so they can focus on specific types of data, or subsets of data from a particular experiment. Keep focused on what’s important to your research…
  10. 10. | 10 How does Pathway Studio help your research?
  11. 11. | 11 Pathway Studio saves you time
  12. 12. | 12 According to our customers…
  13. 13. Pathway Studio versus similar tools
  14. 14. | 14 Pathway Studio vs the Competition: Autophagy 101 175 39 91 20 34 16 73* MetaCore Pathway Studio - Raw Ingenuity Pathway Studio - Corrected Proof Point: More content translates to more results for researchers Adapted figure from Lorenzi et al, 2014. Used with permission. Lorenzi P, Claerhout S, Mills GB, Weinstein JN. 2014 A curated census of autophagy-modulating proteins and small molecules. Autophagy 10:7, 1-11 0 50 100 150 200 250 300 350 400 450 MetaCore IPA Pathway Studio Unique Shared * - This data comes from early 2013. When the list of 73 “unique” IPA hits were checked in PS in July 2014, more than 50 were now found – that’s the power of more content! Some proteins and small molecules are found with all solutions (shared), and each product finds some unique interactions (unique). But Pathway Studio finds 2-3X more than IPA, and 10X more than MetaCore.
  15. 15. Pathway Studio vs the Competition: Apoptosis Apoptosis results similar to Autophagy Ingenuity Pathway Analysis Pathway Studio Lorenzi et al., 2015 unpublished 3487 2894 484 0 1000 2000 3000 4000 5000 6000 7000 IPA Pathway Studio Unique Shared Pathway Studio finds twice as many total results as Ingenuity, and 7X more unique results
  16. 16. | 16 Why researchers need Pathway Studio More content equals more confidence in your answers:  Data collected from 5-8 times more full-text articles provides the needed context and evidence to unravel even the most complex biological processes  Weekly updates - keeps researchers up-to-date with the latest research  Largest collection of expertly-curated reference pathways provides a starting point for complex model building and exploration Analysis tools that provide deeper insights, better understanding  Import your own content to leverage legacy data and in-house expertise  Analysis wizards streamline everyday analysis, highlight most regulated genes in minutes  Advanced tools support creating de novo pathways from customer’s experimental data to enable better ROI
  17. 17. Sample Pathway Studio use cases
  18. 18. | 18 Target discovery • Most comprehensive knowledgebase enables more complete mapping of in-house or public expression data to pathways • Simple data importing using step-by- step wizards • SubNetwork Enrichment Analysis (SNEA) helps identify upstream regulators of specific expression patterns • Drug mechanism of action models facilitate identification of on-target and off-target effects Most researchers use Pathway Studio to analyze in-house experiments
  19. 19. | 19 Biomarker discovery • Most comprehensive knowledgebase, along with cellular localization data provides more information on potential biomarkers. • Easily find and visualize interactions of genes and proteins with specific cell processes, diseases, and small molecules • Linkages with other Elsevier products (Reaxys, PharmaPendium) provide more information about potential and observed biomarkers Biomarkers are a critical early step in many discovery strategies
  20. 20. | 20 Drug repurposing • Largest knowledgebase of drug targets coupled with knowledge on biology of more than 6000 diseases provides the most information to search for shared patterns • Statistical enrichment analysis simplifies identification of common regulators and pathways • Combine multiple disparate pathways to create a comprehensive picture of drug action in the context of each disease, and better understand off-target effects Comprehensive pathways help identify alternative applications
  21. 21. | 21 NGS data interpretation • Import, filter, and analyze VCF data, as well as RNA-Seq data, from any NGS platform • Filter thousands of variations down to a few important ones by comparison to databases of mutational information and predictive tools • The largest collection of literature- derived molecular function data enables more precise associations of mutations with functional effects and disease associations Interpret gene mutations and gene expression information
  22. 22. Sample Pathway Studio workflow
  23. 23. | 23 A blank canvas for your work Starting out…
  24. 24. | 24 Working with search results…
  25. 25. | 25 Building a pathway…
  26. 26. | 26 Building a pathway…
  27. 27. | 27 Cleaning things up
  28. 28. Basic NGS workflow
  29. 29. | 29 • Import and analyze NGS expression (RNA-Seq) data • Browse the Database for specific variations  Find a gene associated with a specific disease  Find deleterious SNPs within a conserved coding sequence • Analyze a single genotype sample  Place affected genes into a new pathway  Find pathogenic variants of a particular gene • Analyzing multiple genotype samples  Find mutations that differ between control and experimental groups Support for the most common NGS analysis workflows
  30. 30. | 30 1. Import VCF file from disk or URL – await confirmation Simple VCF file import
  31. 31. | 31 Once you have 1 or more VCF files loaded, you can browse them for various features Browse the mutation database for specific features
  32. 32. | 32 VCF files can also be searched for specific features Search the database for mutations of interest
  33. 33. | 33 You can search for associations and functional impact Easily identify mutations with probably negative impact
  34. 34. | 34 Compare data across multiple experimental and controls. Filter by location, gene, disease, frequency, etc. NGS workflows: compare multiple genotypes
  35. 35. Professional Services Projects
  36. 36. | 36 Pathway Studio custom services engagements Customized analyses, bespoke datasets/pathways can be performed by our dedicated teams of PhD scientists • Access to life science data and content with proven data curation, taxonomy expertise, and semantic backbone across R&D and post market launch • Demonstrated R&D data integration expertise • Existing life science portfolio of solutions across development spectrum • Global sales footprint in life science sector Partnered with Pathway expert Dr. Phil Lorenzi  Create an expert view on your area  Compares across data types
  37. 37. • The Process: The Professional Services team created a custom search in full-text literature to find statements indicating that the piece contained information about protein mutations. This was then integrated into a custom cartridge for Pathway Studio. • The Results: More than 100,000 mutations were found in the literature. Using Pathway Studio, the customer can search the list and find mutation they needed — and the search strategies will keep the their data set up-to-date. 37 Example: Custom data sets for targeted discovery Challenge: Find all of the reported mutations in cancer cells.
  38. 38. Questions?

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