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International Annotation and SANBI

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

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International Annotation and SANBI

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  1. Genomic activities for Glossina at SANBI2006Win Hide, Mario Jonas and the SANBI team, University of the Western CapeSouth Africa

  2. 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

  3. Genomic Resource and EST management

  4. GO annnotation InterProScan interpro2go Annot8er_blast2GO Translated seqs BLAST KOGS, EGO, TOGs etc ESTScan (D. mel) Map2SunGear GOTerm Lists Gene Lists Translated seqs

  5. Library specific GO assignments regulation of locomotion adult behavior G-protein coupled receptor protein signaling pathway receptor binding signal transduction signal transducer activity transmission of nerve impulse focal adhesion formation receptor antagonist activity DNA binding epidermal growth factor receptor signaling pathway female germ-line sex determination pheromone metabolism regulation of epidermal growth factor receptor signaling pathway transcription factor activity eye morphogenesis morphogenesis of a polarized epithelium cuticle biosynthesis Wnt receptor signaling pathway zinc ion binding methyl-CpG binding histone deacetylase binding NuRD complex polytene chromosome

  6. Evolutionary Scope morsitans palpalis submorsitans pallidipes D.melangaster Anopheles spp.

  7. Training

  8. 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.

  9. 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

  10. 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

  11. 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?

  12. 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

  13. Future • Translational efforts • Consortium management • Communication • Data management • Distribution • Publication strategies

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