Creating Gene Sets from HPO Terms


This tutorial shows how to generate a gene set, based on an input list of HPO terms, and save the set in Mosaic for future analysis.

The steps followed in the above video are described in brief below for the following set of HPO terms (used in the clin.iobio publication: fetal akinesia sequence (HP:0001989), arthrogryposis multiplex congenita (HP:0002804), macrocephaly at birth (HP:0004488), nephrolithiasis (HP:0000787), and pulmonary hypoplasia (HP:0002089).

  1. Click on Applications (or Launch App button on many Mosaic pages)
  2. Select the genepanel.iobio application and click Launch
  3. Type or paste a clinical note or list of HPO terms in the text field and click Submit to the right
  4. The entered HPO terms will be automatically selected, but other associated terms may be available for selection if desired. The GTR and Phenolyzer resources can also be used, but are omitted here, where we are restricting ourself to HPO terms
  5. Click the Generate gene list button to generate a list of genes from the supplied HPO terms
  6. When the list is complete, we are presented with a summary of the search. Click the HPO tab to see options for limiting the size of the gene list
  7. In this example, no gene intersects with more than 3 of the given HPO terms. We can interact with the Overlapping HPO terms chart to select only those genes that intersect with 3, or greater than 2 HPO terms etc. Choosing only genes that intersect with the maximum 3 HPO terms results in 19 genes that can be interogated in the list
  8. Having selected the genes that we are interested in, we can save them as a gene set in Mosaic by clicking the Save Analysis button at the top right of the screen.
  9. Returning to Mosaic, we can see this Gene Set by moving to the Genes page (from the left menu), then clicking on the Sets tab
  • Learn how to use these gene sets in gene.iobio here.