international annotation and sanbi
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Genomic activities for Glossina at SANBI 2006 Win Hide, Mario Jonas and the SANBI team, University of the Western Cape South Africa. International Annotation and SANBI. USA : Promoter element signatures and anatomically restricted expression with the Allen Institute for Brain Science - PowerPoint PPT PresentationTRANSCRIPT
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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
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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
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Genomic Resource and EST
management
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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
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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
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Evolutionary Scope
morsitansmorsitans
submorsitans
submorsitans
palpalispalpalis
D.melangasterD.melangaster pallidipespallidipes
Anopheles spp.Anopheles spp.
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Training
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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.
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Web based resource
•Mario Jonas MSc [email protected]
•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
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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
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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?
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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
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Future
•Translational efforts
•Consortium management
•Communication
•Data management
•Distribution
•Publication strategies