Gene lists

VarSome Clinical offers 4 ways of creating a new gene list:

  1. Copy and modify an existing gene list
  2. Create a new gene list
  3. Create a gene list from HPO (human phenotype ontology) phenotypes
  4. Create a gene list from diseases

 

 

1. Copy and modify an existing gene list

Gene lists can be copied and edited. Clicking on will make a copy of  a gene list.  

This copy can be modified by clicking on : genes can be added or removed. Once you have finished editing the gene list, you can save the list either with the original name or with a new one.

2. Create a new gene list


  • Click on “Create new gene list”.
  • A pop up form window appears, you just need to write a name for your gene list and paste the list of genes that you want to analyse. Important note: the gene names need to follow the HGNC (Hugo Gene Nomenclature Committee) standard (http://www.genenames.org/), if the gene names do not follow this rule you will get an error message after clicking on Save list.

 

3. Create a gene list from phenotypes

    • Click on ”Create gene list from phenotypes”
    • Start by filling in a phenotype.

    • Click on phenotype from the drop down menu to add it to your phenotypes list. (You can right click any phenotype to remove it from the list).
    • Select one or more phenotypes from your list to view the associated genes.

    • Finally select one or more genes to be added to your gene list

     

    The methodology to generate a gene list from phenotype(s) has been changed. Previously, when making a gene list from phenotypes, we would include only those genes that are directly annotated with that phenotype. We have now extended this and instead first collect all diseases linked to the phenotype and then all genes linked to those diseases, as well as any genes directly linked to the phenotype. We already worked this way when adding phenotypes to analyses, so this change ensures we are consistent and also makes sure we don’t miss any genes when creating gene lists.

       

    4.  Create a gene list from diseases

    • Click on ”Create gene list from diseases”
    • Start by filling in a disease.
    • Click on disease from the drop down menu to add it to your diseases list. (You can right click any disease to remove it from the list)
    • Select one or more diseases from your list to view associated genes.
    • Finally select one or more genes to be added to your list.

    Browsing through gene lists

    • Search gene lists by name:

    • Toggle custom view:

     

    • Display gene lists sorted by name or update date:

     

    Edit an existing gene list

    Gene lists can be edited and copied. Clicking on the "Copy" button will make a copy of a gene list.

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    Genes can be added or removed by clicking on the edit button. Once you have finished editing the gene list, you can save the list with either with the original name or with a new one.

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