Gene lists

VarSome Clinical and VarSome Pro offer 3 ways of creating a new gene list:

  1. Create a new gene list
  2. Create a gene list from HPO (human phenotype ontology) phenotypes
  3. Create a gene list from diseases

Create a gene list

  1. To 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 copy-paste the list of genes that you want to analyse. Important note: the gene names need to follow the Hugo Gene Nomenclature Committee standard. If the gene names do not follow this rule, you will get an error message after clicking on Save list.
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  2.   Create a gene list from phenotypes

    • Click on 
    • “Start filling in a phenotype”, ex. blu, mac, hea ...  or HPO term/number

                  

    • You now have the option to select (by clicking) multiple items from the matched phenotypes, clicking on CTRL + left click of your mouse.

    • You can also now remove individual phenotypes / diseases by right clicking on the item you want to remove. Click on blue info icon to find explanation of functionality:

    As soon as you have gathered the phenotypes you wish to create a gene list with, proceed with the remaining steps as shown below:

     

    Note: 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.

       

    3.  Create a gene list from diseases

    • Click on Create gene list from diseases
    • Follow the instructions:

    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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