Bioinformatics Toolbox™

getrelatives (geneont)

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

Syntax

RelativeIDs = getrelatives(GeneontObj, ID)
[RelativeIDs, Counts] = getrelatives(GeneontObj, ID)

... = getrelatives(..., 'Height', HeightValue, ...)
... = getrelatives(..., 'Depth', DepthValue, ...)
... = getrelatives(..., 'Levels', LevelsValue, ...)
... = getrelatives(..., 'Relationtype', RelationtypeValue, ...)
... = getrelatives(..., 'Exclude', ExcludeValue, ...)

Arguments

Return Values

Description

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

[RelativeIDs, Counts] = getrelatives(GeneontObj, ID) also returns the number of times each relative 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.

... = getrelatives(..., 'PropertyName', PropertyValue, ...) calls getrelatives 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:

... = getrelatives(..., 'Height', HeightValue, ...) searches up through a specified number of levels, HeightValue, in the gene ontology. HeightValue is a positive integer. Default is 1.

... = getrelatives(..., 'Depth', DepthValue, ...) searches down through a specified number of levels, DepthValue, in the gene ontology. DepthValue is a positive integer. Default is 1.

... = getrelatives(..., 'Levels', LevelsValue, ...) searches up and down through a specified number of levels, LevelsValue, in the gene ontology. LevelsValue is a positive integer. When specified, it overrides HeightValue and DepthValue.

... = getrelatives(..., '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).

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

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 24316 Terms.

2. Retrieve the immediate relatives for the mitochondrial membrane GO term with an identifier of 31966.

   relatives = getrelatives(GO,31966,'levels',1)
   
   relatives =
   
           5740
           5741
           5743
          31090
          31966
          44429
          44455

3. Create a subordinate Gene Ontology.

   subontology = GO(relatives)
   
   Gene Ontology object with 7 Terms.

4. 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:0005740 --> mitochondrial envelope
   GO:0005741 --> mitochondrial outer membrane
   GO:0005743 --> mitochondrial inner membrane
   GO:0031090 --> organelle membrane
   GO:0031966 --> mitochondrial membrane
   GO:0044429 --> mitochondrial part
   GO:0044455 --> mitochondrial membrane part

5. View relationships of the subordinate Gene Ontology using the biograph function and methods and color the mitochondrial membrane GO terms red.

   BG = biograph(cm, get(subontology.Terms, 'name'));
   BG.nodes(acc==31966).Color = [1 0 0];
   view(BG)

   

6. Retrieve all relatives for the mithocondrial outer membrane GO term with an identifier of 5741.

   relatives = getrelatives(GO,5741,'levels',inf);
   

7. Create a subordinate Gene Ontology.

   subontology = GO(relatives)
   
   Gene Ontology object with 28 Terms.

8. View relationships using the biograph functions.

   [cm acc rels] = getmatrix(subontology);
   BG = biograph(cm, get(subontology.Terms, 'name'));
   BG.nodes(acc==5741).Color = [1 0 0];
   view(BG)

See Also

Bioinformatics Toolbox™ functions: geneont (object constructor), goannotread, num2goid

Bioinformatics Toolbox methods of geneont object: getancestors, getdescendants, getmatrix

getrelatives (biograph)

isdag (biograph)