Difference between revisions of "Needs Analysis Workshop/Report-out Day1"
From phenoscape
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− | === | + | ===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 |
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− | === | + | ===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=== |
− | * | + | * 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 |
Revision as of 16:33, 19 September 2007
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
- 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