Curation of Biological Interactions in FlyBase

1. Curation of Biological Interactions in FlyBase Chihiro Yamada FlyBase Department of Genetics, University of Cambridge, UK. Curator Meeting talk Milwaukee Oct 03

2. Harvard • Genome Annotation(including data from literature) • Expression Patterns(transcripts, proteinsreporter constructs) • Transgenes & Insertions • Sybase Database • Molecular Interactions • Cambridge • Phenotypic DataGenes, alleles, aberrations, transgenes, • insertions • Genetic • Interactions • GO Curation • Sequence Curation • Bibliographic Data • Indiana • Public Web servers • Images • People List • Stocks • Berkeley • Genome Annotation • GadFly Database Curator Meeting talk Milwaukee Oct 03

3. Talk Plan • Interaction curation in FlyBase • Phenotype curation • Genetic interaction curation • Other interaction curation in FlyBase Curator Meeting talk Milwaukee Oct 03

4. Interaction Data in FlyBase • Allele level phenotypic interaction • Gene level interaction • GO IPI and IGI • Molecular interactions Curator Meeting talk Milwaukee Oct 03

5. Phenotype Curation • Allele level curation includes: sequence variants transgene constructs RNAi experiments • Annotated with: Phenotypic class CV Bodypart CV Free text Curator Meeting talk Milwaukee Oct 03

6. Phenotypic Class • 96 terms e.g. • lethal • sterile • behavioural • circadian rhythm defective • locomotor rhythm defective • eclosion rhythm defective • learning defective • cytokinesis defective Curator Meeting talk Milwaukee Oct 03

7. Anatomy CV • 5,835 terms e.g. • adult central nervous system • wing • alula • abdominal 1 neuroblast t2 Curator Meeting talk Milwaukee Oct 03

8. Example of phenotypic class curation RelE20Mutant adults are highly susceptible to infection by E.coli (survival rate is reduced after pricking with an infected needle compared to survival rate of control flies). Mutant adults are not highly susceptible to infection by M.luteus. ( Leulier et al., 2000) Phenotypic class = immune response defective Curator Meeting talk Milwaukee Oct 03

9. Example of body part phenotype curation Fas2e86 “A mutant allele of Fas2 (e86) … leads to (an) increase in synaptic sprouting.” ( Schuster et al., 1996 ) Phenotype body part affected = synapse Curator Meeting talk Milwaukee Oct 03

10. How is this extended to deal with genetic interactions? Relationships between gene products in Drosophila are often studied by combining multiple mutant alleles and examining the phenotypic consequences Curator Meeting talk Milwaukee Oct 03

11. Stronger mutant phenotype Alleles X1 + Y2 Alleles X1 + Z3 Enhancement Mutant phenotype of allele X1 Suppression Wild-type Fly Curator Meeting talk Milwaukee Oct 03

12. Example of phenotypic interaction curation The addition of spz4 enhances the susceptibility of RelE20 mutants to E.coli and M.luteus infection. ( De Gregorio et al., 2002 ) RelE20: Phenotypic class = immune response defective Genetic interaction = immune response defective, enhanceable { spz4 } spz4: Genetic interaction = enhancer, immune response defective { RelE20 } Curator Meeting talk Milwaukee Oct 03

13. Classes of interaction • suppressor suppressible • enhancer enhanceable • non-suppressor non-suppressible • non-enhancer non-enhanceable Curator Meeting talk Milwaukee Oct 03

14. How much of this type of data do we have? • 2,235 genes with GI lines • 58,382 GI lines in total 8,301 alleles • 3,659 enhancement • 4,556 suppression • 6,631 class • 5,348 anatomy Curator Meeting talk Milwaukee Oct 03

15. Interaction Data in FlyBase • Allele level phenotypic interaction • Gene level interaction • GO IPI and IGI • Molecular interactions Curator Meeting talk Milwaukee Oct 03

16. Gene level statements • Can be linked to allele level interaction statements or be based on author statements, e.g. • hh, hedgehog • Interacts genetically with: ptc (data from hhMrt) • Interacts genetically with: rho • 1,934 genes with gene level statements (10,680 lines) Curator Meeting talk Milwaukee Oct 03

17. GO IPI & IGI FlyBase has246 genes with IGI lines126 genes with IPI lines • 458 IGI and 228 IPI lines in total e.g. Nc, Nedd2-like caspase apoptosis ; GO:0006915 | inferred from genetic interaction with FLYBASE:th; FB:FBgn0003691 apoptotic program ; GO:0008632 | inferred from physical interaction with FLYBASE :Ice; FB:FBgn0019972 • All GO associated DBs curate with IGI and IPI Curator Meeting talk Milwaukee Oct 03

18. New Molecular Interaction Curation • 2 types of entity • Objects (~550 so far) • e.g. Notch intracellular domain • Events (~500 so far) • e.g.”Notchless binds to the Notch intracellular domain” • Protein/protein • Protein/DNA • Protein/RNA Curator Meeting talk Milwaukee Oct 03

19. Molecular interactions • Curated from literature • Objects mapped to the genome • Annotated with CVs • location/stage/GO • Plans to incorporate large scale datasets • e.g. 2-Hybrid screens Curator Meeting talk Milwaukee Oct 03

20. Interactions… • Genetic assays • Molecular assays Curator Meeting talk Milwaukee Oct 03

21. Genetic Assays • Strengths • A single screen can find interactions regardless of molecular type. • Generally good evidence of in vivo functional interaction • Weaknesses • Cannot distinguish between direct interactions and presence in a single pathway. • Complex phenotypes can be difficult to interpret Curator Meeting talk Milwaukee Oct 03

22. Molecular assays Strengths • Proof of direct interaction Weaknesses • Often difficult to prove interactions exist in vivo and functionally important Curator Meeting talk Milwaukee Oct 03

23. We need to warn computational biologists! • Curation methods are necessarily based on experimentation • Interpretation of these data must be based on an understanding of the limitations of experimental data Curator Meeting talk Milwaukee Oct 03

24. FlyBase-Cambridge is: Michael Ashburner Rachel Drysdale Becky Foulger Aubrey de Grey Gillian Millburn David Sutherland Chihiro Yamada Thanks to everyone in FlyBase, and fellow DB curators everywhere… Curator Meeting talk Milwaukee Oct 03