vectorbase a resource centre for invertebrate hosts of human pathogens bob maccallum imperial...

VectorBaseVectorBase

VectorBase

A Resource Centre for A Resource Centre for Invertebrate Hosts of Human Invertebrate Hosts of Human

PathogensPathogens

Bob MacCallumBob MacCallum

Imperial College LondonImperial College London


Outline

• Introduction to VectorBase

• Two important recent developments:

– Community Annotations

– Gene Expression Data


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


Why VectorBase?

• Sequencing initiatives do not include “after-care”

• Ensembl had no long-term plans for insects


Main VectorBase activities

• www.vectorbase.org:– Browse, search & download genomic data

• Genome annotation– Automatic & manual

• Functional genomics

• Ontologies

• Training/outreach/consultancy


Invertebrate vectorsSpecies Disease Status Funder

Aedes aegypti Yellow feverDengue fever

Complete† NIAID

Anopheles gambiae PEST Malaria Complete† -

Anopheles gambiae M & S form

Malaria Assembled NHGRI

Culex pipiens quinquefasciatus

Lymphatic filariasis

Complete† NIAID

Glossina morsitans morsitans

Sleeping sickness Initiated Wellcome Trust

Ixodes scapularis Lyme disease Draft gene set NIAID

Lutzomyia longipalpis Leishmania Planned NHGRI/Wellcome Trust

Pediculus humanus Typhus Draft gene set NHGRI

Phlebotomus papatasi Leishmania Planned NHGRI/Wellcome Trust

Rhodnius prolixus Chagas disease Initiated NHGRI


Who is VectorBase?

US

UK

GR


Notre Dame

PIsFrank Collins, Dave Severson, Greg Madey, Nora Besansky

Tasks project coordinationcore website developmentcommunity annotation pipelineAedes and Anopheles community reps.


EBI(European Bioinformatics Institute)

PIEwan Birney

Tasks “automated” genome annotationcomparative genomicsGenbank submissionsgenome browser technology


IMBB, Crete

PIKitsos Louis

Tasks ontologies for anatomy, insecticide resistance, biological processespopulation genetics


Harvard

PIBill Gelbart

Tasks manual annotation


Imperial College, London

PIsGeorge Christophides, Fotis Kafatos

Tasks functional genomics: gene expression, RNAi phenotypes


UC Riverside

PIPeter Atkinson

Tasks Culex pipiens


Purdue University

PICatherine Hill

Tasks Ixodes scapularis


A quick tour of VectorBase

Blast

Genome

browser

Searchengine

BioMart

Downloads


VectorBase genome browser


Genome annotation cycle

Automatic gene build

Assembly

Community annotations

Manual annotations

Other genomes, gene sets

Repeat library (TEs etc)ESTs, cDNAs

Protein domains


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


Community annotation

• Expertise from around world

• Gene models, symbols, literature, function

• Need system to track contributions

• Incorporated in gene build updates

• Credit sourcesCommunity Annotation Pipeline (CAP)


CAP: gene model submission

• Gene symbol• Gene description• mRNA sequence• Translation start• Translation stop• Determination method• GO IDs• PubMed IDs

Excel spreadsheet


CAP: what happens next

• Transcript aligned to genome

• Gene model constructed

• Reviewed by community representative


CAP: other annotations

• Publications

• CV/ontology terms

• Free text comment*

(* unmoderated)


Expression data

• Many microarray technologies

• Many experimental designs

• Large amount of information

• Many ways to do analysis


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


Microarray pipeline at VB

What Where

Alignments & gene assignments Ensembl-style database

Microarray data, raw & processed BASE

Statistics and web interface VB’s GESOL API


Web interfacePPO*


Overall picture of

expression


Genome browser integration


Help & Documentation


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’s future directions

• More genomes & sequencing

• Population biology, association studies

• More community involvement in genome annotation

• Enhanced functional genomics resources


Acknowledgements

• VB team

• IC PIs

• VB SWG

• NIAID

• Community

• Organisers

• Audience

vectorbase a resource centre for invertebrate hosts of human pathogens bob maccallum imperial...

Documents