2. Pathway analysis Daniel Hurley

3. Pathway analysis: summary A popular buzzword… but what does it mean? A popular buzzword… but what does it mean? How do you do it? How do you interpret the results?

4. First

5. What we mean by ‘pathway analysis’ A ‘pathway’ implies causation, but don’t be fooled!

6. What we mean by ‘pathway analysis’ A ‘pathway’ implies causation, but don’t be fooled! Most ‘pathway analysis’ actually identifies groups of functionally similar transcripts. Louis’ example: (http://gather.genome.duke.edu/)

7. A useful paper…. What we mean by ‘pathway analysis’ But the conclusion is: lots of tools, some quite different approaches!

8. Pathway analysis tools like GATHER, DAVID, and GeneSetDB typically rely on enrichment analyses to tell us things. This set of techniques asks the question ‘of this set of genes, how many share any particular function, and is that more than we would expect by chance?’ Example: the top 200 most differentially-expressed genes by some ranking (e.g. adjusted p-value) Determination of ‘by chance’ is usually done using a permutation (= Monte Carlo) approach Other ‘pathway analyses’ involve signatures of groups of transcripts (e.g. using Principal Component Analysis) What we mean by ‘pathway analysis’

9. But what do we mean by a ‘function’? Lots of things: Protein function Hypothetical protein function Chromosomal location Metabolic pathway association Disease association

10. Daunting

11. The key point

12. Pathway analysis can identify common features present in a group of transcripts What the output means depends on the specific biology under study No such thing really as a ‘general’ pathway analysis A good place to start is by finding papers relevant to the specific biology What we mean by ‘pathway analysis’

13. What can you do with it? Some answers: Get a general picture of the active functions in a condition (vs. control) Investigate whether a particular function is active in a condition Differentiate conditions by their active functions Investigate the functions associated with a particular gene Identify conditions with similar functions

14. Next

15. Begin with a list of transcripts of interest Pathway analysis: how you do it

16. Choose a web-based tool: GATHER, DAVID and GeneSetDB are good ones to start Pathway analysis: how you do it But Pathguide.org has 325 pathway links at last count

17. Enter the list of transcripts: with most tools, you will either paste in gene names or identifiers, or upload a file Pathway analysis: how you do it

18. Finally

19. Basic tools will produce ranked lists of the most ‘enriched’ categories: Pathway analysis: interpreting results GATHER

20. More sophisticated ones will produce ‘network’ diagrams Pathway analysis: interpreting results DAVID Ingenuity Pathways Analysis But the interpretation of these is rather subjective

21. Summary Pathway analysis should probably be called information enrichment analysis – a more accurate term Used prudently, it is a useful tool for exploring the functional landscape of an experiment To make it meaningful, you need to interpret the results in the context of the specific biology under study There are a lot of web-based tools; start with one which is current and produces a result you value To start, you need a set of (transcripts) of interest To present the results, you can use a simple table, or a more complex ‘network’ diagram Risk: false-positives are very difficult to identify, and with enough data you can link any molecular species to any other species

22. FIN Any questions?