Melland/PhenoLinker

PhenoLinker Visualization

Interactive visualization tool for PhenoLinker. PhenoLinker is a system capable of associating a score to a phenotype-gene relationship and to provide an explanation for the predicted score. PhenoLinker provides an embedding for each gene and phenotype of 64 dimensions, and then it produces and score with the given embeddings.

This application is focused on the genes from the intellectual disability Genomics England amber panel: https://panelapp.genomicsengland.co.uk/panels/285/. For each gene on the left panel of the application, the user can select the phenotypes such that the gene-phenotype association is not found in the HPO Ontology, version December 2022, and such that the score produced by PhenoLinker is greater than 0.9. When we select a gene and a phenotype and press the Go! button, this application retrieves the score for the given link and then it shows:

• —A bar plot with the 10 most important attributes (genes and phenotypes), divided in 5 groups: phenotype attributes (dimensions of the phenotype descriptions embeddings), expression attributes, ExAC attributes, locus attributes, protein attributes and genomic information attributes.

• —A table with the 64 specific attributes of the selected gene.

• —Two 3D scatter plots that represents the embeddings generated by PhenoLinker using the t-SNE algorithm. One of the plots shows all phenotypes with a color gradient that represents the score of the relationship with the selected gene. The other plot shows all the genes with a color gradient that represents the score for the relationship with the selected phenotype.

Authors

• —Main developer: Jose Luis Mellina Andreu (joseluis.mellinaa@um.es)
• —Technical supervisor: Alejandro Cisterna García (alejandro.cisterna@um.es)
• —Technical supervisor: Juan Antonio Botía Blaya (juanbot@um.es)