Difference between revisions of "Phenoscape use cases"
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==Comparison of genetically and evolutionarily correlated characters== | ==Comparison of genetically and evolutionarily correlated characters== | ||
===Motivation=== | ===Motivation=== | ||
| − | + | For phylogenetic systematics, one would like to know if two or more characters show phylogenetic correlation due to an underlying genetical/developmental correlation. One way to address this is to determine if changes to both (all) those characters are found in a single-gene zebrafish mutant. [The reverse of this use case can be imagined--[[User:Tjvision|Tjvision]] 12:55, 15 August 2008 (EDT)] | |
===Example=== | ===Example=== | ||
| − | + | The user observes a suite of changes in the size of the dentary, maxilla, ceratohyal, and opercle bones that support the monophyly of a particular clade. The user queries the system for zebrafish mutant phenotypes in which two or more of the above anatomical terms are used. Phenoscape returns sox9ahi1134, in which the the dentary, opercle, and maxilla bones are reduced in size relative to wild-type, whereas other bones are relatively unaffected. [This seems like a variant on the first use case with multiple Es and no Qs, so perhaps these can be combined --[[User:Tjvision|Tjvision]] 12:55, 15 August 2008 (EDT)] | |
===Input=== | ===Input=== | ||
| − | Multiple phenotype search specifications: entity, quality, etc., representing the evolutionary character changes. Option to match exactly or to match descendant terms (as in quality "count", above). | + | Multiple phenotype search specifications: entity, quality, etc., representing the evolutionary character changes. Option to match exactly or to match descendant terms (as in quality "count", above). |
===Output=== | ===Output=== | ||
| − | A list of ZFIN mutant identifiers and associated genes which are associated with phenotypes matching | + | A list of ZFIN mutant identifiers and associated genes which are associated with phenotypes matching 2 or more of the search criteria. [The output should at least be a matrix of genes against phenotypes --[[User:Tjvision|Tjvision]] 12:55, 15 August 2008 (EDT)] |
==Map changes of an evolutionary character on a phylogeny== | ==Map changes of an evolutionary character on a phylogeny== | ||
Revision as of 16:55, 15 August 2008
Contents
- 1 Identify zebrafish candidate genes for an evolutionary phenotype
- 2 Identify evolutionary changes that match the phenotype of a zebrafish mutant
- 3 Comparison of genetically and evolutionarily correlated characters
- 4 Map changes of an evolutionary character on a phylogeny
- 5 View values for a particular character for a set of species with some value for another character
- 6 View all species with multiple phenotypes matching a condition
- 7 View every change in an anatomical structure mapped on a tree
- 8 Find morphological hot spots
Identify zebrafish candidate genes for an evolutionary phenotype
Motivation
To obtain one or more candidate genes for an evolutionary change in phenotype, one would like to know which genes, when perturbed in a model organism, give rise to a "similar" phenotypic difference between wildtype and mutant genotypes.
Example
User observes evolutionary variation among fishes in the size of the ceratobranchial 5 bone. User queries Phenoscape for matching mutant zebrafish phenotypes using Entity = Ceratobranchial 5 [from TAO] and all qualities pertaining to attribute ‘size’ [from the PATO]. The response is a list of zebrafish mutants and their phenotypes, along with the associated genes, and possibly gene expression images, in this case for genes such as sox9a, since there is a size reduction in ceratobranchial 5 in the mutant line sox9ahi1134.
Input
A phenotype search specification: entity (TAO), quality (PATO). Option to match exactly or to match descendant terms (as in quality "size", above).
Output
A list of ZFIN mutant identifiers with matching phenotype of each, associated gene, perhaps gene expression images (or links to).
Identify evolutionary changes that match the phenotype of a zebrafish mutant
Motivation
It would be of interest to identify phenotypic variation among wild species that could plausibly arise from changes in the same gene that is perturbed in particular zebrafish mutant.
Example
User observes a reduction in number of branchiostegal rays in a zebrafish mutant for the gene endothelin-1. The user wants to know whether branchiostegal ray number is variable among fish species, and if so, what is the pattern of change across fish evolution. User queries Phenoscape using Entity = Branchiostegal rays [from TAO] and all qualities pertaining to attribute ‘count’ [from the PATO]. Phenoscape returns a list [just a list?--Tjvision 12:40, 15 August 2008 (EDT)] of taxa and phenotypes. The user would see that all cypriniforms, including zebrafish, have three branchiostegal rays, but other fishes, including close ostariophysan relatives, have higher and lower numbers. [How would a list achieve that? Should this not be mapped on a phylogeny? --Tjvision 12:40, 15 August 2008 (EDT)]
Input
A phenotype search specification: entity, quality, etc. Option to match exactly or to match descendant terms (as in quality "count", above).
Output
A list of matching evolutionary phenotypes and the taxon for each. [A list is too crude - the phenotypes need to be phylogenetically mapped in some way--Tjvision 12:40, 15 August 2008 (EDT)]
Motivation
For phylogenetic systematics, one would like to know if two or more characters show phylogenetic correlation due to an underlying genetical/developmental correlation. One way to address this is to determine if changes to both (all) those characters are found in a single-gene zebrafish mutant. [The reverse of this use case can be imagined--Tjvision 12:55, 15 August 2008 (EDT)]
Example
The user observes a suite of changes in the size of the dentary, maxilla, ceratohyal, and opercle bones that support the monophyly of a particular clade. The user queries the system for zebrafish mutant phenotypes in which two or more of the above anatomical terms are used. Phenoscape returns sox9ahi1134, in which the the dentary, opercle, and maxilla bones are reduced in size relative to wild-type, whereas other bones are relatively unaffected. [This seems like a variant on the first use case with multiple Es and no Qs, so perhaps these can be combined --Tjvision 12:55, 15 August 2008 (EDT)]
Input
Multiple phenotype search specifications: entity, quality, etc., representing the evolutionary character changes. Option to match exactly or to match descendant terms (as in quality "count", above).
Output
A list of ZFIN mutant identifiers and associated genes which are associated with phenotypes matching 2 or more of the search criteria. [The output should at least be a matrix of genes against phenotypes --Tjvision 12:55, 15 August 2008 (EDT)]
Map changes of an evolutionary character on a phylogeny
Motivation
After observing variation of a trait in evolution (as found in use case #Identify evolutionary changes that match the phenotype of a zebrafish mutant, a biologist may further want to know what the pattern of evolution of this trait has been. This can lead to hypotheses relating to how often this trait changes in evolution, such as whether such changes occur in parallel at many places on the evolutionary tree.
Example
A biologist observes in number of branchiostegal rays across taxa in the database (such as in the results of #Identify evolutionary changes that match the phenotype of a zebrafish mutant). The biologist maps the character changes on a phylogeny, and sees that all cypriniforms, including zebrafish, have three branchiostegal rays, but other fishes, including close ostariophysan relatives, have higher and lower numbers (McAllister, '68). Specifically, reduction in number has occurred multiple times; solenostomids and syngnathids (ghost pipefishes and pipefishes), giganturids, and saccopharyngoid (gulper and swallower) eels have the fewest branchiostegal rays (McAllister, '68).
Input
A list of taxa and their phenotypes for a previously searched character specification. A phylogenetic tree including the taxa of interest.
Output
A graphical representation of a phylogenetic tree (cladogram). The branches are colored to represent reconstructed ancestral states of the given character values (or ambiguity). The state reconstruction is performed using a standard algorithm such as parsimony or a maximum likelihood method.
View values for a particular character for a set of species with some value for another character
Motivation
A particular phenotype change may have evolutionary consequences for another aspect of phenotype. This may be because they are linked via developmental or physical constraints, or are related through their effect on natural selection.
Example
A biologist observes a number of species missing the parietal bone. It appears that these species are also generally small in size. The biologist searches for all species in the database which lack the parietal bone. He then requests the body length value for all those species.
Input
A phenotype search specification for the phenotype to match. A second phenotype search specification for the attribute for which to search for values.
Output
A table containing a list of taxa matching the first entered phenotype. A second column in the table presenting the value of each taxon for the second entered character.
View all species with multiple phenotypes matching a condition
Example
A biologist wants to list all the species that have lost more than one bone. Or more specifically, all species that have lost more than one bone in the head.
Input
A phenotype search specification, with constraints on the entity term such as "is_a term1" and "part_of term2". The threshold number of annotations matching the phenotype required to include a taxon.
Output
A list of taxa and their phenotypes matching the input criteria.
View every change in an anatomical structure mapped on a tree
Motivation
A biologist may be interested in how a particular structure has evolved, without knowing what types of changes have occurred in that structure. It would be useful to view the pattern of evolution of all phenotypes involving that structure, visualized on a phylogeny as in #Map changes of an evolutionary character on a phylogeny.
Example
A biologist is interested in the parietal bone. She chooses this term from the anatomy ontology and then views a phylogeny displaying all reconstructed character transitions involving the parietal as an entity.
Input
An anatomical term from an anatomy ontology. A phylogeny containing the species of interest.
Output
A listing of all phenotypes for each species which contain the entered term as an entity. A display of the phylogeny mapping changes for each phenotypic character.
Find morphological hot spots
Motivation
Some parts of anatomy may evolve rapidly relative to others. These can be identified as those that exhibit many evolutionary changes in phenotype. This could be a simple metric like finding anatomical terms that exhibit many different value states for characters. A more complex analysis might perform ancestral state reconstruction for every character in the database, and return the entity terms involved in phenotypes with the most transitions.
Example
A biologist may be interested to know whether structures that evolve rapidly share any genetic commonality. The biologist obtains a list of rapidly evolving structures using this query, and then performs further analyses of those structures.
Input
All phenotypes in the database.
Output
A list of anatomy terms exhibiting the highest number of phenotypes or changes, depending on the metric.
