Difference between revisions of "Needs Analysis Workshop/Report-out Day1"

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===Phylogenies: Report-out===
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===Evo Group report-out===
  
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* ability to choose from the phylogenies in the database
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* need to improve ontologies, e.g. for describing behavior
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** even with the possibility of constructing a consensus tree
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* need to improve tools for analyzing images
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** ability to move branches around
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* covariance of entities, attributes
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** choose a subset (pruned phylogeny)
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* broader queries of entities within particular constraints, such as structures
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* map character changes onto the phylogeny
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* need capacity to store media (e.g., images, movies)
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** choose a feature of interest, e.g. by entity
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* need environmental, ecological, and geographical data
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** issues of visualizing many characters on a branch
 
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* link to genes
 
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** e.g. show genes with elevated expression
 
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** need to be careful about showing statistics -  may be misused
 
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* BLAST-like similarity search for how a trait (or trait change) maps across a tree
 
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** for example, a user has discovered elevated expression of a gene in certain branches of the tree; are there phenotypes that are similar to this distribution?
 
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* Questions that this might be used for
 
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** Evolvability
 
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** Constraints
 
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** Parallel evolution
 
  
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===Phenotype correlation: Report-out===
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===Devo Group report-out===
  
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* matrix showing numerical summaries
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* identifying homologies among distantly related taxa
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** traits vs traits, traits vs genes, genes vs genes
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** for example, do fishes have digits? E.g., if genes have similar effects on fins as on digit development.
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** cells would be number of branches on which the two traits change in common (traits vs traits), or number of mutants they have in common (traits vs traits, and traits vs genes), or number of traits in common (genes vs genes)
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* patterns of covariation
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** problem of whether to use entity alone, entity and attribute (character), or EQ (character state)
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** for example, cusps on mammalian teeth
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** problem of opening a can of worms by offering too detailed of an analysis, especially if it involves ancestral state reconstruction using phylogenies
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** could be used to identify "character modules" that are well-connected
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** e.g., is limblessless associated with elongation
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** connections within modules should be more stable than between
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* tree view
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* for a branch hypothesized to be under positive selection (from e.g. a molecular analysis), identify candidate phenotypes that could have been selected for
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** highlight terminal taxa or phylogenies for bringing up a matrix for
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** map synapomorphies onto a phylogeny
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* body-plan view
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** identify phenotypes with highest rate of change on that lineage
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** highlight different areas and ask for traits affecting all of those
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** needs phylogeny that is selectable and manipulable
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** highlight different areas and then map the corresponding and correlated traits onto a tree
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* use the database to point out holes in the knowledge
  
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===Semantics: Report-out===
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===Discussion===
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[[Image:Day2-brainstorming1.whiteboard.JPG|thumb|right|384px|Analysis Pipeline, Character Modules]]
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* enrichment analysis: given a list of genes, which phenotype terms are overrepresented among them
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* capturing representing variation seems to be a general problem and challenge, but critically needed
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** variation in regulatory (or morphogenic) gene expression and corresponding phenotypic changes (Hox gene expression example)
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** polyphenism: variability of phenotype that can distinguish species but is also  dependent on environmental factors or variable levels of gene expression
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** do we need to capture frequencies for polymorphisms to represent variability
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** there are morphological differences even between inbred strains, for example for JAX mouse strains in cranial morphology
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* integrating with genomic resources:
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** linking out to genome databases seems mandatory
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* alerting features
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** for example, saving queries as RSS feeds
  
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* most queries aren't complex, and often simply want to have a list (e.g., genes, phenotypes)
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[[Category:Needs Analysis Workshop]]
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** for this, complex semantics may not be needed
 
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** shallower ontologies, or higher-level (more general) terms may largely suffice
 
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* searching or analyzing phenotypes by similarity would require more rigorous or deep semantics
 
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* too fine grained ontologies may be problematic for annotation
 
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* allelic links:
 
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** emerging dataset of genetic mutations that are proven to have caused evolutionary change (D. Stern)
 
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** directionality of allelic changes may be important
 
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** may need an evolves-from (develops-from?) relationship
 

Latest revision as of 20:04, 18 January 2008

Evo Group report-out

  • need to improve ontologies, e.g. for describing behavior
  • need to improve tools for analyzing images
  • covariance of entities, attributes
  • broader queries of entities within particular constraints, such as structures
  • need capacity to store media (e.g., images, movies)
  • need environmental, ecological, and geographical data

Devo Group report-out

  • identifying homologies among distantly related taxa
    • for example, do fishes have digits? E.g., if genes have similar effects on fins as on digit development.
  • patterns of covariation
    • for example, cusps on mammalian teeth
    • could be used to identify "character modules" that are well-connected
    • connections within modules should be more stable than between
  • for a branch hypothesized to be under positive selection (from e.g. a molecular analysis), identify candidate phenotypes that could have been selected for
    • map synapomorphies onto a phylogeny
    • identify phenotypes with highest rate of change on that lineage
    • needs phylogeny that is selectable and manipulable
  • use the database to point out holes in the knowledge

Discussion

Analysis Pipeline, Character Modules
  • enrichment analysis: given a list of genes, which phenotype terms are overrepresented among them
  • capturing representing variation seems to be a general problem and challenge, but critically needed
    • variation in regulatory (or morphogenic) gene expression and corresponding phenotypic changes (Hox gene expression example)
    • polyphenism: variability of phenotype that can distinguish species but is also dependent on environmental factors or variable levels of gene expression
    • do we need to capture frequencies for polymorphisms to represent variability
    • there are morphological differences even between inbred strains, for example for JAX mouse strains in cranial morphology
  • integrating with genomic resources:
    • linking out to genome databases seems mandatory
  • alerting features
    • for example, saving queries as RSS feeds
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