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

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Presentation transcript:

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

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

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

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

VectorBase Main VectorBase activities –Browse, search & download genomic data Genome annotation –Automatic & manual Functional genomics Ontologies Training/outreach/consultancy

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

VectorBase Who is VectorBase? US UK GR

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.

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

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

VectorBase Harvard PI Bill Gelbart Tasks manual annotation

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

VectorBase UC Riverside PI Peter Atkinson Tasks Culex pipiens

VectorBase Purdue University PI Catherine Hill Tasks Ixodes scapularis

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

VectorBase VectorBase genome browser

VectorBase VectorBase genome browser

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

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

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)

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

VectorBase

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

VectorBase

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

VectorBase

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

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

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

VectorBase Web interface PPO*

VectorBase

Overall picture of expression

VectorBase

Genome browser integration

VectorBase Help & Documentation

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

VectorBase

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

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