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).
We have a Youtube-Channel with several tutorial videos, e.g.
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.
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.
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!
The cross species phenotype resource (called uberpheno) has been developed in the context of the Monarch Initiative.
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.