XOMICS FIRST MEETING June 17th 2005

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X-OMICS FIRST MEETINGJune 17th 2005

• Bioinformatics Workpackage
• And
• Related Issues
• Frederic Brunet
• Nicolas Pollet
• Mike Gilchrist

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Agenda - I

• REPORTS
• Status of genome assembly (MG)
• Expansion of EST collection clustering (MG)
• Full length insert sequencing (MG)
• Annotation jamboree, Cambridge (MG)
• Xenbase (NP)
• Online resources (NP)

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Agenda - II

• DISCUSSIONS
• Co-ordinating data between sites (MG)
• Ontologies (NP)
• Xenopus resource portal (MG/NP)
• Orthologous gene sets (MG/FB)
• Comparing X. laevis and X. tropicalis (FB/MG)

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Status of genome assembly

• JGI Genome Assembly v3
• v4 will be released in late July
• Mostly long range joins
• End-sequencing large inserts
• Very useful even if not complete
• Maybe 90 of genes
• Sequence is on fragments scaffolds
• Not complete enough for chromosomes
• Much finishing could be done
• But very useful for gene structure

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Expansion of EST collection clustering

• 2004 400,000 ESTs
• 2005 JGI sequenced 325,000 more clones
• 600,000 ESTs
• 450,000 released to GenBank
• Many diverse libraries, 20,000 per
• Esp. adult tissues metamorphosis stage
• The current one million ESTs have been clustered
  (MG) and are awaiting release from JGI
• Milestone!
• 40,000 clusters
• 40,000 singletons
• (14,000 EF1-alpha)

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Full length insert sequencing

• Full length cDNAs
• 2883 Xenopus tropicalis MGC
• 6000 from Wellcome FL project
• 4100 sequenced (some overlap)
• 3100 validated FL
• 1920 more from JGI currently being sequenced at
  Stamford (some overlap)
• 5000 more in pipeline
• Cloning vector is significant pCS107/8
• Sanger will sequence some more

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Annotation jamboree, Cambridge

• July 11th 15th Sanger Institute
• Annotate 4,100 cDNA sequences
• Mark ends of ORF
• Identify genes (functional annotation)
• Exons on genomic sequence - ?
• Should have partially automated genome annotation
• Issues
• Identify genes from Mouse/Human/many??
• Concerns about accuracy
• Gene symbols style?
• More annotation in September/October - JGI

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Xenbase

• Primarily concerned with community information
  and literature annotation
• Collaboration
• Avoid duplication of effort

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Online resources

• There is a lot of Xenopus data out there

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Agenda - II

• DISCUSSIONS
• Co-ordinating data between sites (MG)
• Ontologies (NP)
• Xenopus resource portal (MG/NP)
• Orthologous gene sets (MG/FB)
• Comparing X. laevis and X. tropicalis (FB/MG)

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Co-ordinating data between sites

• Why?
• What data is there?
• Where is it? And who owns it?
• Gene-centric
• Key Words Ontologies
• Data sharing and access
• Centralised vs. Distributed

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What? Where? Who?

• Related data is kept in various separate
  databases
• It would undoubtedly be useful to be able to ask
  questions of the entire dataset at once
• Find me all the genes that are expressed
• For this gene find all the mutant phenotypes
• Need to identify what there is
• How its managed
• Is it accessible
• Who owns it
• What long terms plans for it are

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Gene-centric

• How to reach a state where we can compare data
  between different databases using a gene
  identity?
• Annotation will help
• Gene symbols may be unreliable
• Sequence is best!
• Wont happen on its own

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Key Words Ontologies

• There are other sets of information that must be
  consistent between databases for co-ordination to
  work
• Must be consistently able to describe (for
  instance) where in the organism and at what stage
  of development some observed effect has taken
  place
• Key words vs ontologies

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Data sharing and access

• Public Data
• Shareable Data
• Private Data
• Make sure the technological effort is not
  disproportionate
• What are the timescales?

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Centralised vs. Distributed

• Three pots of the same type of data
• E.g. in situ expression data
• Assuming all the experimental and informational
  problems have been dealt with, what are our
  options?
• Amalgamate the data
• Distributed model

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Centralised
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Distributed
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Ontologies

• The glue that holds data sets together

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Xenopus resource portal

• A single point of reference
• Links to all the key Xenopus resources
• But with some idea of the sort of data to be
  found, and how to use it

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Orthologous gene sets

• For each Xenopus gene find the gene that has the
  same function (!?) in other model organisms
• N.b. potential difference between sequence
  ortholog and functional ortholog
• What might this resource be good for?
• Frederic

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Comparing X. laevis and X. tropicalis

• Frederic
• Looking for pairs of X. laevis genes