Bioinformatics Toolbox™

getdescendants (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, ...)

Arguments

`GeneontObj`	A geneont object, such as created by the `geneont` function.
`ID`	GO term identifier or vector of identifiers.
`DepthValue`	Positive integer specifying the number of levels to search downward in the gene ontology.
`RelationtypeValue`	String specifying the relationship types to search for in the gene ontology. Choices are: `'is_a'` `'part_of'` `'both'` (default)
`ExcludeValue`	Controls 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).

Return Values

`DescendantIDs`	Vector of GO term identifiers including `ID`.
`Counts`	Column vector with the same number of elements as terms in `GeneontObj`, indicating the number of times each descendant is found.

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 tallying counts in gene enrichment studies. For more information, see the Gene Ontology Enrichment in Microarray Data demo.

... = 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 string. 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).

Examples

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 24316 Terms.
```

Retrieve the descendants of the mithochondrial respiratory chain GO term with an identifier of 5746.

descendants = getdescendants(GO,5746)

descendants =

        5746
        5747
        5749
        5750
        5751
       42652
       42653

Create a subordinate Gene Ontology.

subontology = GO(descendants)

Gene Ontology object with 7 Terms.

Create a report of the subordinate Gene Ontology terms.

[cm acc rels] = getmatrix(subontology);
rpt = [num2goid(acc) get(subontology.Terms, 'name')]';
disp(sprintf('%s --> %s\n',rpt{:}))

GO:0005746 --> mitochondrial respiratory chain
GO:0005747 --> mitochondrial respiratory chain complex I
GO:0005749 --> mitochondrial respiratory chain complex II
GO:0005750 --> mitochondrial respiratory chain complex III
GO:0005751 --> mitochondrial respiratory chain complex IV
GO:0042652 --> mitochondrial respiratory chain complex I, peripheral segment
GO:0042653 --> mitochondrial respiratory chain complex I, membrane segment

View relationships of the subordinate Gene Ontology using the biograph function and methods.
```
BG = biograph(cm, num2goid(acc));
view(BG)
```