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Gene Panels

In this section, you can add gene panels so that you can filter the discovered variants by them. The gene panel is a set of genes of interest (for example, genes associated with a specified phenotype).

To open the section with gene panels, go to the "Gene panels" page from the "Settings" page block through the navigation panel on the left:

Add a gene panel#

There are four ways to add a panel to the system:

  1. Selection of genes of interest from all genes (by name or Ensembl ID);
  2. Adding genes associated with a certain phenotype;
  3. Import of a pre-prepared gene list;
  4. Import panel from the library of the most common clinical panels.
tip

When adding a panel, the first and second ways can be combined.

1. Adding genes from the list of all genes to the panel#

  1. Click on to open the form of adding a gene panel:

  1. In the opened form, enter gene panel name in the Name field. You can also add a panel description.

  2. Add genes to the panel. To do this, enter an official gene symbol or an Ensembl gene ID (ENSGxxxxxxxxxxx) in the search field.
    From the list of matching genes, select one or more genes, click the corresponding row (or rows), and then click . Alternatively, you can add a gene by double-clicking its row.

You can search within the genes added to the panel and remove genes from the panel. To remove a gene, either double-click its row or select one or more rows and click .

  1. After you have added all the needed genes to the panel, click on . A gene panel will be added to the system.

2. Adding genes from ontology to the panel#

  1. Click on to open the form of adding a gene panel:

  1. In the opened form, enter gene panel name in the Name field. You can also add a panel description.

  2. Click on . You will see the search dialog to find terms from the Human Phenotype Ontology (HPO) and the Mondo Disease Ontology (Mondo). The dialog displays the main phenotype groups in a drop-down list:

  1. Search and select phenotypes in one of the following ways:
  • Search directly in the drop-down list. You can navigate the phenotype groups using the and buttons to expand and collapse the list of terms within each group, respectively:

You can also search for a phenotype or disease:

  • by its full or partial name;
  • by its HPO ID (for example, HP:0009733 or 0009733);
  • by its Mondo ID (for example, MONDO:0009733 or 0009733).

For example, searching for "glioma" returns several matching terms:

To select a term, click the corresponding row. You can select either an entire phenotype group or an individual phenotype. After selecting a phenotype (for example, Glioma), its information card is displayed:

The left side of the card displays the full phenotype or disease name with a link to the corresponding page in the HPO or Mondo ontology (provided by the Monarch Initiative), as well as all available information from the selected ontology, including the description, synonyms, comment, and PubMed references.

The center of the card displays the term hierarchy. Parent terms of the selected disease (in this example, Glioma) are shown above it, indicating the phenotype groups to which it belongs. Child terms (phenotypes and diseases that belong to the Glioma group) are displayed below.

The right side of the card contains a list of genes associated with the selected phenotype or disease. These genes will be included in the gene panel when selecting a term.

Above the phenotype card, the selected terms are displayed together with their ontology identifiers. The number of genes associated with each term is shown in parentheses. To open a phenotype card, click the corresponding term. To remove a term, click the button:

  • Search using the term hierarchy. The phenotype card allows you to navigate through the ontology hierarchy. Click the name of a parent or child phenotype to open its card.
    If the term has not yet been selected and associated genes are available, click to include those genes in the panel.

  • Search in multi-select mode. Click the right button of the search mode switcher in the upper-left corner of the dialog: . A list of the main phenotype groups with selection checkboxes is displayed.

Search can be performed:

  • by full or partial name;
  • by HPO ID (for example, HP:0009733 or 0009733);
  • by Mondo ID (for example, MONDO:0009733 or 0009733).

For example, searching for "glioma" returns several matching terms:

In multi-select mode, you can select multiple terms simultaneously from the drop-down list. To select a phenotype, activate its corresponding checkbox.

When you have finished selecting phenotypes, click anywhere outside the drop-down list but within the search dialog. The selected filter terms are displayed at the top of the dialog. The number of genes associated with each phenotype is shown in parentheses. Click a phenotype to open its information card. To remove a phenotype, click the button.

To close the phenotype search dialog without adding ontology-associated genes to the panel, click or anywhere outside the dialog.

To add genes associated with the selected phenotypes to the panel, click .

The added genes are displayed in the list on the right. You can search within the list or remove genes from the panel. To remove a gene, select it in the list and then click :

  1. After you have added all the needed genes to the panel, click on . A gene panel will be added to the system.

3. Import gene list#

  1. Click on to open the form of importing gene list:

  1. In the opened form, enter gene panel name in the Name field. You can also add a panel description.

  2. Enter a list of genes in the Genes field. The list must contain official gene symbols and/or Ensembl gene IDs (ENSGxxxxxxxxxxx), separated by commas or line breaks.
    If multiple Ensembl gene IDs correspond to the specified gene symbol in the database (for example, because the gene is annotated on both the primary assembly and one or more alternative sequences), all corresponding genes are added to the panel. For example, adding the gene MUC6 includes three genes to the panel: ENSG00000184956, ENSG00000277281, and ENSG00000277518.

  3. Click on to add gene panel to the system.

4. Import gene panel from library#

  1. Click on to open the form of importing gene panel:

  1. In the opened form, tick the required panels:

  1. Click on .

Edit a gene panel#

To add or remove genes from the added panel, click on the panel row on the "Gene panels" page. In the opened form, you can change the name and description of the panel, remove and add genes to the panel (you can add genes either from the list of all genes or from ontology). After making changes click on .

Delete a gene panel#

To remove a gene panel from the system, hover over its row on the "Gene panels" page and click on the appeared button.