1. VectorBase A Resource Centre for Invertebrate Hosts of Human Pathogens Bob MacCallum Imperial College London

2. VectorBase Outline Introduction to VectorBase Two important recent developments: –Community Annotations –Gene Expression Data

3. VectorBase What is VectorBase? Aim  Genomic bioinformatics resource for invertebrate vectors of human pathogens  Data hub for community Funding  US NIAID (National Institute for Allergy and Infectious Diseases)  via its Bioinformatics Resource Centre (BRC) program

4. VectorBase Why VectorBase? Sequencing initiatives do not include “after-care” Ensembl had no long-term plans for insects

5. VectorBase Main VectorBase activities www.vectorbase.org: –Browse, search & download genomic data Genome annotation –Automatic & manual Functional genomics Ontologies Training/outreach/consultancy

6. VectorBase Invertebrate vectors SpeciesDiseaseStatusFunder Aedes aegyptiYellow fever Dengue fever Complete†NIAID Anopheles gambiae PESTMalariaComplete†- Anopheles gambiae M & S formMalariaAssembledNHGRI Culex pipiens quinquefasciatusLymphatic filariasisComplete†NIAID Glossina morsitans morsitansSleeping sicknessInitiatedWellcome Trust Ixodes scapularisLyme diseaseDraft gene setNIAID Lutzomyia longipalpisLeishmaniaPlannedNHGRI/Wellcome Trust Pediculus humanusTyphusDraft gene setNHGRI Phlebotomus papatasiLeishmaniaPlannedNHGRI/Wellcome Trust Rhodnius prolixusChagas diseaseInitiatedNHGRI

7. VectorBase Who is VectorBase? US UK GR

8. VectorBase Notre Dame PIs Frank Collins, Dave Severson, Greg Madey, Nora Besansky Tasks project coordination core website development community annotation pipeline Aedes and Anopheles community reps.

9. VectorBase EBI (European Bioinformatics Institute) PI Ewan Birney Tasks “automated” genome annotation comparative genomics Genbank submissions genome browser technology

10. VectorBase IMBB, Crete PI Kitsos Louis Tasks ontologies for anatomy, insecticide resistance, biological processes population genetics

11. VectorBase Harvard PI Bill Gelbart Tasks manual annotation

12. VectorBase Imperial College, London PIs George Christophides, Fotis Kafatos Tasks functional genomics: gene expression, RNAi phenotypes

13. VectorBase UC Riverside PI Peter Atkinson Tasks Culex pipiens

14. VectorBase Purdue University PI Catherine Hill Tasks Ixodes scapularis

15. VectorBase A quick tour of VectorBase Blast Genome browser Search engine BioMart Downloads

16. VectorBase VectorBase genome browser

17. VectorBase VectorBase genome browser

18. VectorBase Genome annotation cycle Automatic gene build Assembly Community annotations Manual annotations Other genomes, gene sets Repeat library (TEs etc) ESTs, cDNAs Protein domains

19. VectorBase Manual annotation Flybase team (Kathy Campbell) Anopheles 2L completed Sep 2006 Anopheles 2R completed Sep 2007 Anopheles X completed Feb 2008 875 Culex genes completed July 2008 Three mosquitoes better than one

20. VectorBase Community annotation Expertise from around world Gene models, symbols, literature, function Need system to track contributions Incorporated in gene build updates Credit sources  Community Annotation Pipeline (CAP)

21. VectorBase CAP: gene model submission Gene symbol Gene description mRNA sequence Translation start Translation stop Determination method GO IDs PubMed IDs Excel spreadsheet

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23. CAP: what happens next Transcript aligned to genome Gene model constructed Reviewed by community representative

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30. CAP: other annotations Publications CV/ontology terms Free text comment* (* unmoderated)

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32. Expression data Many microarray technologies Many experimental designs Large amount of information Many ways to do analysis

33. VectorBase Microarray repositories Widely adopted standard: MIAME GEO (NCBI) & ArrayExpress (EBI) Repository ≠ Useful data Curation backlog at central repositories VectorBase data is manageable We manage and curate

34. VectorBase Microarray pipeline at VB WhatWhere Alignments & gene assignmentsEnsembl-style database Microarray data, raw & processedBASE Statistics and web interfaceVB’s GESOL API

35. VectorBase Web interface PPO*

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37. Overall picture of expression

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40. Genome browser integration

41. VectorBase Help & Documentation

42. VectorBase No time today for… Averaging over multiple reporters Ambiguous reporters List of microarray experiments in VB Community microarray data submission Expert analysis & collaboration Future developments

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44. VectorBase’s future directions More genomes & sequencing Population biology, association studies More community involvement in genome annotation Enhanced functional genomics resources

45. VectorBase Acknowledgements VB team IC PIs VB SWG NIAID Community Organisers Audience