Up: Component summary
Up: Component summary
Component
GOSearchFilters 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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