PhenogramViz is a tool that automatically analyses and visualizes gene-to-phenotype relations for a set of genes affected by CNV of a patient and a set of HPO-terms representing the symptoms of said patient. The tool makes full use of the cross-species phenotype ontology “uberpheno” (see here).


Video Tutorials

We have a Youtube-Channel with several tutorial videos, e.g.

  • How to install PhenogamViz: Video
  • How to prepare your data: Video
  • How to get from your data to a phenogram: Video
  • Prioritzation of CNVs: Video
  • Phenogram: Internal data and external links: Video
  • Export and saving of your results: …

Please not that you have to turn on the video captions in Youtube. There is no sound in these videos!


Download and install Cytoscape Version 3.1.0. (PhenogramViz is not compatible to earlier versions of Cytoscape) Download the jar-file (below) and Select App->Install from file and point the program to the downloaded jar-file.

Example data

PhenogramViz requires two datasets. At first you have to define the the symptoms of the patient (i.e. a set of HPO-term-IDs). Second of all you have to define the set of copy-number variant regions in the patients genome.

  1. Symptoms
    • Enter them directly in PhenogramViz
    • Create a file with the HPO-term IDs. Must look like this: download example patient symptoms
  2. Copy-number variant regions
    • Load lists of regions (defined by Chromosome + Start + End (+ type)
    • Load lists of genes


Current version: PhenogramViz (0.1.3) - This jar-file can then be installed in Cytoscape.

Previous: PhenogramViz (0.1.2).


Please cite this paper when using PhenogramViz!

Phenotype data

The cross species phenotype resource (called uberpheno) has been developed in the context of the Monarch Initiative.

Data from paper

The data used in the paper can be found here.

This contains the uberpheno ontology (crossSpeciesPheno.obo), the gene-phenotype annotations (HSgenes_crossSpeciesPhenoAnnotation.txt), and the used CNVs (testedBenignCnvs.txt, testedPathogenicCnvs.txt). For the pathogenic CNV we also show the associated HPO-terms.