OVERVIEW
Once you have list of genes associated with the gene, you might want to further filter the list to narrow down on a subset of genes with certain characteristics. This article describe the available options for filtering such a gene set.
STEPS
Note | A user action, such as click or enter, is italicized.A visible item on the platform, such as a [link] or a [button], is in square brackets.A link to another article or external source is underlined. |
1. Scroll and click to select filter options on the left. See the end of article for more details on the filters.
2. Click the [Apply] button to apply the selected filter(s). One or more filters can be selected at a time.
Note | Clicking the [Reset] button will clear the selection. |
3. The list of genes on the right is shown based on the applied filter(s). The number of results refers to the number of genes in the set based on the applied filter(s).
Note | The applied filter options are automatically added to the [Set Description] field.The gene set can be filtered at a later stage again if applicable in [Sets] |
4. Click the [Save] button to save the set. The saved gene set can be found in [Sets] folder.
Note | Change the Set name to be more specific. By default, the Set name is formatted as followed: <start concept><category><date><time>Add a tag to the set to easily locate it at a later point. |
Details on filter options
There are three way to filter the gene set related to a gene (gene as the search term):
1) Filter based on the characteristics of the related genes (Note: these filters are always available for gene sets):
| Filter option | If selected, then only include |
| Taxonomy | genes in the selected taxonomy class |
| Gene classification | genes in the selected gene class* |
| Gene location | genes with the selected subcellular location* |
| Tissue expression | genes with the specified expression level in selected tissue* |
| Gene cell type expression | genes with the specified expression level in selected cell type* |
| Chemical antagonist | genes with gene products that contain a chemical antagonist with the specified maximum IC50 |
| Chemical agonist | genes with gene products that contain a chemical agonist with the specified maximum IC50 |
| Tool compounds | genes that have tool compounds |
| Known drug targets | genes that are known drug targets |
*Multi-selection is allowed.
2) Filter based on how genes in the set are functionally related to the searched gene (Note: these filters are only available if the search concept is a single gene):
| Filter Option (Relation Filters) | If selected, then only include |
| Direct protein interaction | genes that binds with | forms protein complex with | controls state change of | controls phosphorylation of the searched gene |
| Transcription factors | genes that are classified as transcription factor |
| Functional inhibition | genes that inhibit the searched gene |
| Functional stimulation | genes that stimulate the searched gene |
| Functional inhibited | genes that are inhibited by the searched gene |
| Functionally stimulated | genes that are stimulated by the searched gene |
3) Filter based on evidence: filter based on the number of publication and databases references with co-occurence for the searched gene and related genes.
Possible next steps
- Analyze the filtered gene set in [Analytics] and [Relation Map]
Related resources
- How does Search work?
- How to perform a gene search?
- How to identify genes associated with a gene?
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