Genomic activities for Genomic activities for Glossina at SANBIGlossina at SANBI

20062006

Win Hide, Mario Jonas and the SANBI team, Win Hide, Mario Jonas and the SANBI team, University of the Western CapeUniversity of the Western Cape

South AfricaSouth Africa

International Annotation and SANBI•USA : Promoter element signatures and anatomically restricted expression

with the Allen Institute for Brain Science

•USA : NIH funded Baboon cDNA annotation project

•USA: NIH funded HIV genome annotation

•Japan: H-INV human cDNA clustering and annotation with the Genome

Network Project (GNP), Japan

•Japan: Fantom3 consortium, Japan, with the role of promoter annotation

and gene expression annotation between mouse and man

•Japan: GNP and Fantom4 we perform data integration, analysis, and

comparison of gene expressoin between mouse and human to include

determination of promoter element signatures related to expression states.

•Japan : Rice Annotation Project 3 (RAP3) promotor annotation for stress-

response genes

•UK/USA/Japan/South Africa: IGGI cDNA clustering and GO annotation

Genomic Resource and EST

management

GO annnotation

Annot8er_blast2GO Annot8er_blast2GO

InterProScaninterpro2go

InterProScaninterpro2go

Translated seqs

BLAST KOGS, EGO, TOGs etc

BLAST KOGS, EGO, TOGs etc

ESTScan (D. mel) ESTScan (D. mel) Translated seqsMap2SunGearMap2SunGear GOTerm ListsGene Lists

GOTerm ListsGene Lists

Library specific GO assignments

focal adhesion formationreceptor antagonist activityDNA bindingepidermal growth factor receptor signaling pathwayfemale germ-line sex determinationpheromone metabolismregulation of epidermal growth factor receptor signaling pathwaytranscription factor activityeye morphogenesis morphogenesis of a polarized epithelium cuticle biosynthesisWnt receptor signaling pathwayzinc ion binding

regulation of locomotionadult behaviorG-protein coupled receptor protein signaling pathwayreceptor bindingsignal transductionsignal transducer activitytransmission of nerve impulse

methyl-CpG bindinghistone deacetylase bindingNuRD complexpolytene chromosome

Evolutionary Scope

morsitansmorsitans

submorsitans

submorsitans

palpalispalpalis

D.melangasterD.melangaster pallidipespallidipes

Anopheles spp.Anopheles spp.

Training

IGGI satellite meeting• Website development

• Funding

• Integration with Tryp community

• Resources overview

• Formation of MOUs with participating institutions

• Working principles for the scientific endeavour

• Planning and sharing of information around the genome sequencing; and

• Reporting on the outcomes relative to the genome from the recent IGGI led training meeting in CT.

Web based resource

•Mario Jonas MSc mario@sanbi.ac.za

•EST and GO analysis

•Data curator and website manager• username = surname+first_letter_of_first_name e.g. M Berry = berrym

• Default account details are: username = password

Understanding the Annotation landscape

•Heikki Lehvaslaiho - SANBI•Win Hide - SANBI•Mario Jonas - SANBI•Michael Gaunt - LSHTM/SANBI•Alan Christoffels - TEMASEK•Todd Taylor - RIKEN•Matt Berriman - SANGER•Christiane Hertz-Fowler - SANGER•Michael Ashburner - U Cambridge•Suzi Lewis - Berkeley•Kim Worley - Baylor•Dan Lawson - SANGER

Annotation

•Need a realistic annotation strategy for the vector.•How will data become available.? •How will it initially become annotated•How will it be re-annotated?•How will it be exploited in the African context to

result in control?

Learning from the past

•Drosophila genome project

• Global view

•specific annotation improvements could be targetted fopr IGGI

•Select key gene families and target the BAC sequencing so that more specific sequence analyses can be carried out in parallel

•Technical review

•Access and distribution

Future

•Translational efforts

•Consortium management

•Communication

•Data management

•Distribution

•Publication strategies