Add Genes to Panel

Charlene Son-Rigby -

The Add Genes to Panel page provides several ways to add genes to a panel. Genes can be added individually by gene symbol, from an existing gene set or panel, from HPO Terms and Phevor, or from a chromosomal region.

Navigation

You can reach the Add Genes to Panel page from:
-  Opal Home page  >>  Panel Builder link >> Actions menu >> Curate Panel option  >>  Add Genes button
-  Opal Toolbar  >>  Menu  >>  Panel Builder option >> Actions menu >> Curate Panel option >>  Add Genes button

Features

Select one of the methods to add genes to the panel by clicking on the respective tab header. After entering or selecting the desired genes and click the Add Genes button. A message will be displayed above the tabs to report on the progress. Possible messages include:

Genes added to panel
The entered gene symbol(s) matched the official HGNC symbols and were added successfully to the panel.
Matched # gene(s)
This message provides the count of genes where the symbol entered was a synonym to an official gene symbol which was successfully added to the panel.
Found # gene(s) already in panel
Genes already in the panel are not added to the panel and their count and symbols are reported here.
Could not find # gene(s)
If a symbol is entered that is not the official symbol or synonym for a gene or the biotype of the gene is not a supported Ensembl biotype, the entered symbol is reported here. For supported biotypes see Appendix 6.

Use the Back button to return to the Curate Panel page or add additional genes by any of the 5 methods. 

By Symbol

Enter one or multiple gene symbols into the text field. The text field is limited to 20000 characters.

By Gene Set

If any gene sets of the type My Set are defined in your workspace, a list of these gene sets is displayed here. Select one or more gene sets to add all genes in the selected gene set(s) to the panel. 

From Other Panels

The list of all Workspace Panels is displayed with the Name, ID, Test Code and Gene Count. Add all genes from a panel by checking the Add All checkbox or select individual genes. The Show Genes link will display all genes in the panel with individual checkboxes.

From HPO Terms & Phevor

Search for genes using HPO (Human Phenotype Ontology) terms and Phevor by entering phenotype term in the text field. As you type a dropdown list of matching HPO terms will be displayed. Selecting one of the terms will enter the term into the text field. Continue typing to enter additional terms.

Click on an HPO term in the text field to select it (highlighted in orange). This will display the HPO term's Definition, Synonyms, HPO parent node and HPO Sub-nodes below the text field. Clicking on any of the parent or sub-nodes replaces the highlighted HPO term in the text field.

When all desired terms are entered click the Run Phevor button. Phevor will rank all genes by their association with the selected HPO terms and displays the top 500 ranked genes with their Rank and Phevor Prior. Select the desired genes by checking their checkboxes.

From Chromosome Regions

Specify one or more chromosomal regions in the format chr:start-end to select all genes in the region. The Search Genes dropdown menu allows you to limit the search to OMIM genes with disorders (default selection), OMIM genes with recessive inheritance patternOMIM genes with dominant inheritance pattern, or all genes.

Note: Only genes with supported Ensembl biotypes are added to the panel (see Appendix_6).

 

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