1. the European Nutrigenomics Organisation Using pathway information to understand genomics results Chris Evelo BiGCaT Bioinformatics

2. the European Nutrigenomics Organisation Understanding  Array data Typical procedure 1.Annotate the reporters with something useful (UniProt!) 2.Sort based on fold change 3.Search for your favorite genes/proteins 4.Throw away 95% of the array

3. the European Nutrigenomics Organisation

4. Understanding  Array data Typical procedure 1.Annotate the reporters with something useful (UniProt!) 2.Sort based on fold change 3.Search for your favorite genes/proteins 4.Throw away 95% of the array

5. the European Nutrigenomics Organisation Understanding  Array data “Advanced” procedures oGene clustering or principal component analysis oGet groups of genes with parallel expression patterns oUseful for diagnosis oNot adding much to understanding (unless combined)

6. the European Nutrigenomics Organisation Functional Mapping Annotation/ coupling

7. the European Nutrigenomics Organisation Best known: GenMAPP Full content of GO database Textbook like local mapps Geneboxes with active backpages, coupled to online databases Visualize anything numerical (fold changes on arrays, p-values, present calls, proteomics results)

8. the European Nutrigenomics Organisation GenMAPP: Full GO content

9. the European Nutrigenomics Organisation GenMAPP: Textbook like maps Extensive backpages present with links to online databases

10. the European Nutrigenomics Organisation GenMAPP: visualize anything numerical Example Proteomics results (2D gels with GC-MS identification). Fasting/feeding study shows regulation of glycolysis (data from Johan Renes, UM). Other useful things: - p-values, present calls - presence in clusters - presence in QTLs

11. the European Nutrigenomics Organisation MAPPfinder Ranks mapps where relatively many changes occur Useful to find unexpected pathways Statistics hardly developed (many dependencies to overcome) Next example from heart failure study (Schroen et al. Circ Res; 2004 95: 506-514)

12. the European Nutrigenomics Organisation GenMAPP: Full GO content

13. the European Nutrigenomics Organisation Scientist know GenMapp Advantages: Easy to use, Reasonable visualization Some pathway statistics Interesting content Disadvantages: Small academic initiative, uncertain lifespan No info on reactions, metabolites, location No change (e.g. time course) visualization Content could be better!

14. the European Nutrigenomics Organisation Datasources 1 GenMapp local mapps: Created by a single postdoc (Kam Dahlquist).

15. the European Nutrigenomics Organisation Datasources 2 KEGG: Older pathway database (Kyoto Japan), on enzyme code (EC) level. Annotation problems for automatic annotation (no absolute match between EC and SP ID) Contributed and converted Mapps See example

16. the European Nutrigenomics Organisation Datasources 3 Gene Ontology Database: Simple tree structure database with a lot biological content (biologist know and like it). Automatic annotation possible even for EST’s See structure in GenMapp 1 (or use Go browser)

17. the European Nutrigenomics Organisation Datasources 4 Alternative programs like GeneGo: Based on expert knowledge (20 Russian biochemists). Allows pathway connection (explain) Primitive views of multiple conditions See example results

18. the European Nutrigenomics Organisation Fatty acid oxidation - II

19. the European Nutrigenomics Organisation

20. Datasources 5 Reactome: Curated reactions database (with n- dimensional interconnections) from EBI e.a. Still lacks views and export options

21. the European Nutrigenomics Organisation Proposed workflow Combine and forward existing maps to limited group of experts Text mining from key genes/metabolites Forward improved maps to limited group of experts Collect back page info Forward new draft to a larger group of experts within NuGO Develop storage format plus tools Think of best way to store pathway information Develop/adapt entry tools plus converters Test resulting maps Make maps available Started as a NuGO and IOP gut health initiative. Waiting for expert response. (Add another map) Evaluated some commercial tools (pathway assist).

22. the European Nutrigenomics Organisation BioPAX Plus/GMML 2 Storing pathway data Expert data Reactome BioPAX GMML Current GenMapp GenMapp 2 NUGO/EBI EBI BiGCaT/GenMapp Rachel van Haaften (BiGCaT/NuGO) and Marjan van Erk (TNO/NuGO) will visit EBI early 2005 to learn doing this Philippe Rocca and Imre Vastrik (EBI/Reactome) will define a way to get Reactome views and export them to GenMapp2 Rachel van Haaften (BiGCaT/NuGO) and Marjan van Erk (TNO/NuGO) will test this and give user feedback BiGCaT Tue students created GenMapp 2 – GMML converter with help from Lynn Ferrante (GenMapp.org) This step has not been taken care off as of yet… GMML (GenMapp Markup Language) is a superset of BioPAX 1. BioPAX could contain graphical views. (GMML 2 = BioPAX2). But, how do we make that happen?

23. the European Nutrigenomics Organisation Reactome to GenMapp Current status: Export via MS-Access shows only some content (reaction numbers) in GenMapp. Example

24. the European Nutrigenomics Organisation Views on reactions 1 Reaction databases are build from interconnected reactions (pathways). Some of these reactions may connect to other known pathways. Combined pathways may form knew pathways that we didn’t know.

25. the European Nutrigenomics Organisation Views on reactions 2 Unknown pathways may not be connected in the database yet. But they may: 1)Show co-regulation 2)Plus contain regulatory elements (We can’t analyze those from scratch…)

26. the European Nutrigenomics Organisation Challenges Biological concepts and available tools do not yet meet! Biologists: -know what they want -don’t know how to do it or what problems are involved. Computer science people: -know how it should be done -but not what should be done. BMT students have shown to be able to work on the interface