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GOSearch

Filters gene lists based on Gene Ontology annotations. Only genes that are annotated with given GO terms are selected for output. This components takes the parent-child relationships of GO into account: a gene is annotated with a given GO term if it has annotation entries either for the exact GO term or some child term.

You may use GOFilter if you do not want to provide ontology file as an input.

Version 1.1
Bundle microarray
Categories Filter GO
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
bioAnnotation AnnotationTable Mandatory Annotations that are used as the basis for filtering
go Ontology Mandatory Gene ontology database

Outputs

Name Type Description
hits CSV Genes and the matching ontologies

Parameters

Name Type Default Description
geneColumn string "" Name of the gene ID column or an empty string referring to the first ID column of the table
goColumn string "GO" Name of the GO annotation column
numMatches int 1 Required number of matching annotations for the gene to be selected for output. Each GO annotation increments the gene score by one if it has at least one term matching it. The maximum score of each gene is the number of its annotations.
parentFilter boolean false Skip parent terms if the same gene has been annotated with their child.
terms string (no default) Comma-separated list of GO terms that are used for filtering

Test cases

Test case Parameters IN
bioAnnotation
IN
go
OUT
hits
case1 properties bioAnnotation go hits

terms=GO:03,GO:04


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