Gonzalo G ómez, PhD. ggomez@cnio.es

1. Course on Functional Analysis ::: An Introduction to Ingenuity Pathway Analysis. Madrid, Feb 16th, 2010. Bioinformatics Unit Structural Biology and Biocomputing program CNIO Gonzalo Gómez, PhD. ggomez@cnio.es

2. ::: Schedule. Introduction. Running into IPA Quick Search Toolbar Gene Lists IPA Analysis Sharing Projects

3. ::: Schedule. Introduction. Running into IPA Quick Search Toolbar Gene Lists IPA Analysis Sharing Projects

4. ::: Introduction. Ingenuity Pathways Analysis (IPA) Ingenuity Pathways Analysis v8.5 Release Date: Feb 2010 Customer Support: support@ingenuity.com http://www.ingenuity.com/products/pathways_analysis.html Integrated approach to “Omics” analysis :::

5. ::: Introduction. Ingenuity Pathways Analysis (IPA)

6. ::: Introduction. Ingenuity Pathways Analysis (IPA)

7. ::: Introduction. Ingenuity Pathways Analysis (IPA) Types of analysis :::

8. ::: Introduction. Ingenuity Pathways Analysis (IPA) Answering biological questions :::

9. ::: Schedule. Introduction. Running into IPA Quick Search Toolbar Gene Lists IPA Analysis Sharing Projects

10. ::: Web Accession. Ingenuity Pathways Analysis (IPA) https://analysis.ingenuity.com/pa/

11. Project Manager Menu. ::: Running into IPA. Ingenuity Pathways Analysis (IPA)

12. ::: Running into IPA. Ingenuity Pathways Analysis (IPA) File > Preferences :::

13. ::: Help and tutorials. Ingenuity Pathways Analysis (IPA)

14. ::: Help and tutorials. Ingenuity Pathways Analysis (IPA) Help > Tutorials :::

15. ::: IPA Networks Legend. Ingenuity Pathways Analysis (IPA) Help >Legend :::

16. Overlapping Networks Nodes and Edges Network Explorer Tags ::: IPA Networks Legend. Ingenuity Pathways Analysis (IPA) Help >Legend :::

17. ::: Schedule. Introduction. Running into IPA Quick Search Toolbar Gene Lists IPA Analysis Sharing Projects

18. Genes or chemicals Genes/Chemicals associated with Functions/Diseases Genes targeted by Drugs ::: Quick start searching a Single Gene. Ingenuity Pathways Analysis (IPA) GENES: Affymetrix, Agilent, Affymetrix SNP ID, Applied Biosystems, Code Link, Locus Link, Genbank, HUGO, Illumina, UniGene, RefSeq, Uniprot, etc. DRUGS: Systematic names, IUPAC, CAS, Chemical formula Brand Name.

19. Description GO Annotations Human, Mouse, Rat details Database Information (Gene, RNA, Prot.) Functional roles Mutant Information Modifications and regulation Disease Expression and Localization Physical interactions Literature entries Additional findings… ::: Quick start exploring a Single Gene. Ingenuity Pathways Analysis (IPA) Which biological and disease processes are most relevant to my genes of interest?

20. ::: Explore and Advanced Search Options. Ingenuity Pathways Analysis (IPA) How do I query the Ingenuity Pathways Knowledge Base about specific genes, processes, diseases, drugs, famiies or subcellular locations?

21. Description GO Annotations Human, Mouse, Rat details Database Information (Gene, RNA, Prot.) Functional roles Mutant Information Modifications and regulation Disease Expression and Localization Physical interactions Literature entries Additional findings… ::: Quick start exploring a Single Gene. Ingenuity Pathways Analysis (IPA)

22. ::: Quick start exploring a Single Gene. Ingenuity Pathways Analysis (IPA)

23. ::: Quick start exploring a Single Gene. Ingenuity Pathways Analysis (IPA) Interactive gene networks :::

24. ::: Schedule. Introduction. Running into IPA Quick Search Toolbar Gene Lists IPA Analysis Sharing Projects

25. ::: Network Explorer Toolbar. Ingenuity Pathways Analysis (IPA)

26. ::: Network Explorer Toolbar. Ingenuity Pathways Analysis (IPA)

27. ::: Exploring a Single Gene. Ingenuity Pathways Analysis (IPA) Building a pathway :::

28. ::: Network Explorer Toolbar. Ingenuity Pathways Analysis (IPA) Building pathways ::: Grow Path explorer (shorstest path) Connect Trim (remove) Keep (filter) Add Molecule/Relationship Also…quick access:

29. ::: Network Explorer Toolbar. Ingenuity Pathways Analysis (IPA) Building pathways ::: Add molecule relationship Also…quick access:

30. ::: Network Explorer Toolbar. Ingenuity Pathways Analysis (IPA) Overlaying pathways ::: Expression values Drug Functions and diseases My List Canonical pathway My pathway Ingenuity tox list Highlight

31. ::: Network Explorer Toolbar. Ingenuity Pathways Analysis (IPA) Designing pathways :::

32. ::: Network Explorer Toolbar. Ingenuity Pathways Analysis (IPA) View options :::

33. ::: Schedule. Introduction. Running into IPA Quick Search Toolbar Gene Lists IPA Analysis Sharing Projects

34. Gene, drug, AffyID1, Oxal*, CASP*, RefSeq X, cisplatin, … ::: Exploring Gene Lists. Ingenuity Pathways Analysis (IPA) ::: Searching Lists.

35. ::: Gene Lists. Ingenuity Pathways Analysis (IPA) Saving a gene list :::

36. ::: Gene Lists. Ingenuity Pathways Analysis (IPA) Stored gene lists :::

37. What regulatory effects relationships exists between the genes/proteins in my dataset? ::: Gene Lists. Ingenuity Pathways Analysis (IPA) Creating pathways with Gene Lists ::: Etc.

38. ::: Schedule. Introduction. Running into IPA Quick Search Bar Tools Gene Lists IPA Analysis Sharing Projects

39. ::: Analysis using IPA. Ingenuity Pathways Analysis (IPA) Expression data analysis Toxicology analysis Biomarker analysis Metabolomics analysis

40. ::: Types of Analysis. Ingenuity Pathways Analysis (IPA) Core Analysis: Core Analysis allows you to interpret datasets in the context of biological processes, pathways and molecular networks. Core Comparison Analysis: Core Comparison allows you to analyze changes in biological states across time and dosages. First run a core analysis on your multiple datasets that represent multiple timepoints or dosage treatments and use core Comparison Analysis to understand which biological processes and/or diseases are relevant to each timepoint or dose. Tox Analysis: The tox solution allows you to assess toxicity and safety of compounds of interest early in the development process and rapidly understand the relevant toxicity phenotypes and clinical pathology endpoints associated with a dataset. Tox Comparison Analysis: Allows you to analyze changes in relevant toxicity phenotypes and clinical pathology endpointsacross time and dosages. First run a Tox Analysis on your multiple datasets that represent multiple timepoints or dosage treatments, use Tox Comparison Analysis to understand which tox functions and/or pathways are relevant to each timepoint or dose.

41. ::: Types of Analysis. Ingenuity Pathways Analysis (IPA) Biomarker Filter: The biomarker analysis solution allows you to identify and prioritize the most relevant and promising molecular biomarker candidates from datasets from nearly any step of the drug discovery process or any type of disease research. Use the Biomarker Filter to prioritize molecular biomarker candidates based on contextual information such as mechanistic connection to diseases, detection in bodily fluids. Then, use the Biomarker Comparison Analysis to identify biomarker candidates that discriminate between or are common to a disease state and/or drug response. Biomarker Comparison Analysis: To identify biomarker candidates that discriminate between or are common to a disease state and/or drug response. First run the Biomarker Filter to prioritize molecular biomarker candidates based on contextual information such as mechanistic connection to diseases, detection in bodily fluids, and use the Biomarker Comparison Analysis to identify biomarker candidates that discriminate between multiple samples. Metabolomics Analysis: The metabolomics analysis solution allows you to gain biological insight into cell physiology and metabolism from metabolite (endogenous chemicals)data. If you have multiple time points or dosage treatments, use Comparison Analysis to understand which biological processes and/or diseases are relevant to each time point or dose. Metabolomics Comparison Analysis:Comparison Core/ Metabolomics Analysis allows you to compare multiple experimental conditions in the context of biological processes, pathways and molecular networks

42. ::: Importing data for analysis. Ingenuity Pathways Analysis (IPA) File format A ::: • Single observation • .xls datasheet accepted • Up to 18 MB • 50000 row size limit

43. ::: Importing data for analysis. Ingenuity Pathways Analysis 7.1 (IPA) File format B ::: • Multiple observations (up to 10) • .xls datasheet accepted • Up to 18 MB • 50000 row size limit

44. ::: Sample Analyses. Ingenuity Pathways Analysis (IPA) Useful examples to learn how to deal with Ingenuity IPA…

45. ::: Core Analysis. Expression Data Analysis. Ingenuity Pathways Analysis (IPA) Accession and workflow ::: Core Analysis: Core Analysis allows you to interpret datasets in the context of biological processes, pathways and molecular networks.

46. ::: Core Analysis. Expression Data Analysis. Ingenuity Pathways Analysis (IPA)

47. Results tabs ::: Core Analysis. Expression Data Analysis. Ingenuity Pathways Analysis (IPA) Core analysis output ::: Right-tailed Fisher Exact test

48. Right-tailed Fisher Exact test ::: Core Analysis. Expression Data Analysis. Ingenuity Pathways Analysis (IPA) Some statistics ::: 2x2 Contingency Table.  = 0.05 p < 0.05 + FDR are considered significant

49. ::: Core Analysis. Expression Data Analysis. Ingenuity Pathways Analysis (IPA) Results tabs ::: Networks Lists(Tox) Functions(Bio) Overlapping networks Network explorer Canonical Pathways

50. ::: Networks & Canonical Pathways Ingenuity Pathways Analysis (IPA) Which well characterized cell signaling and metabolic pathways are most relevant in my data?