OVERVIEW
Once you have list of genes associated with a disease, 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 disease (disease 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 disease (Note: these filters are only available if the search concept is a single disease)
| Filter option (Relation Filters) | If selected, then only include |
| Tumor expression (only available if the searched disease is a type of cancer) | genes that are expressed in the search cancer |
| Dysregulated proteins | genes with gene products that are downregulated or upregulated in the disease |
Upregulated proteins | genes with gene products that are upregulated in the disease |
| Downregulated proteins | genes that are downregulated in the disease |
| Diseases associated genetic variation | genes with variants (resulting in gene malfunction) that are associated with the disease |
| Diseases causal annotation | genes with variants (resulting in gene malfunction) that causes the disease |
| Animal model for disease | genes with gene product variant that causes, brings about, and are associated with the disease in animal studies |
3) Filter based on evidence: filter based on the publication and databases references of the relation between searched disease 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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