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getdescendants

Class: geneont

Find terms that are descendants of specified Gene Ontology (GO) term

Syntax

DescendantIDs = getdescendants(GeneontObj, ID)
[DescendantIDs, Counts] = getdescendants(GeneontObj, ID)
... = getdescendants(..., 'Depth', DepthValue, ...)
... = getdescendants(..., 'Relationtype', RelationtypeValue, ...)
... = getdescendants(..., 'Exclude', ExcludeValue, ...)

Description

DescendantIDs = getdescendants(GeneontObj, ID) searches GeneontObj, a geneont object, for GO terms that are descendants of the GO term(s) specified by ID, which is a GO term identifier or vector of identifiers. It returns DescendantIDs, a vector of GO term identifiers including ID. ID is a nonnegative integer or a vector containing nonnegative integers.

[DescendantIDs, Counts] = getdescendants(GeneontObj, ID) also returns the number of times each descendant is found. Counts is a column vector with the same number of elements as terms in GeneontObj.

Tip

The Counts return value is useful when you tally counts in gene enrichment studies.

... = getdescendants(..., 'PropertyName', PropertyValue, ...) calls getdescendants with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

... = getdescendants(..., 'Depth', DepthValue, ...) searches down through a specified number of levels, DepthValue, in the gene ontology. DepthValue is a positive integer. Default is Inf.

... = getdescendants(..., 'Relationtype', RelationtypeValue, ...) searches for specified relationship types, RelationtypeValue, in the gene ontology. RelationtypeValue is a character vector. Choices are 'is_a', 'part_of', or 'both' (default).

... = getdescendants(..., 'Exclude', ExcludeValue, ...) controls excluding ID, the original queried term(s), from the output DescendantIDs, unless the term was found while searching the gene ontology. Choices are true or false (default).

Input Arguments

GeneontObjA geneont object, such as created by the geneont constructor function.
IDGO term identifier or vector of identifiers.
DepthValuePositive integer specifying the number of levels to search downward in the gene ontology.
RelationtypeValue

Character vector specifying the relationship types to search for in the gene ontology. Choices are:

  • 'is_a'

  • 'part_of'

  • 'both' (default)

ExcludeValueControls excluding ID, the original queried term(s), from the output DescendantIDs, unless the term was reached while searching the gene ontology. Choices are true or false (default).

Output Arguments

DescendantIDsVector of GO term identifiers including ID.
CountsColumn vector with the same number of elements as terms in GeneontObj, indicating the number of times each descendant is found.

Examples

  1. Download the current version of the Gene Ontology database from the Web into a geneont object in the MATLAB® software.

    GO = geneont('LIVE', true)

    The MATLAB software creates a geneont object and displays the number of terms in the database.

    Gene Ontology object with 27827 Terms.

  2. Retrieve the descendants of the "aldo-keto reductase activity" GO term with a GO identifier of 4033.

    descendants = getdescendants(GO,4033)

descendants =

        4032
        4033
        8106
       32018
       32866
       32867
       46568
       50112
       50236

  3. Create a subordinate Gene Ontology.

    subontology = GO(descendants)

Gene Ontology object with 9 Terms.

  4. Create and display a report of the subordinate Gene Ontology terms, that includes the GO identifier and name.

    rpt = [num2goid(cell2mat(get(subontology.terms,'id')))...
       get(subontology.terms,'name')]';
disp(sprintf('%s --> %s \n',rpt{:}))

GO:0004032 --> aldehyde reductase activity 
GO:0004033 --> aldo-keto reductase activity 
GO:0008106 --> alcohol dehydrogenase (NADP+) activity 
GO:0032018 --> 2-methylbutanal reductase activity 
GO:0032866 --> xylose reductase activity 
GO:0032867 --> arabinose reductase activity 
GO:0046568 --> 3-methylbutanal reductase activity 
GO:0050112 --> inositol 2-dehydrogenase activity 
GO:0050236 --> pyridoxine 4-dehydrogenase activity

  5. View relationships of the subordinate Gene Ontology by using the getmatrix method to create a connection matrix to pass to the biograph function.

    cm = getmatrix(subontology);
BG = biograph(cm,rpt(1,:));
view(BG)

See Also

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