MINERVA 12.2 release
We are happy to announce the new release of MINERVA platform, which hosts the PD map.
Details about the changes and bug fixes can be found in the release notes.
Here, we’d like to highlight the features that the PD map users may find the most interesting.
The plugins button now displays the list of pre-loaded plugins, easy to start and use. Currently available are:
Map exploration allowing to explore the map in a molecule-centric way (see here for a detailed description)
Drug reactions providing a link between the adverse drug reactions and drug targets in the map (see here for a detailed description)
Disease associations linking variants reported by Protein API variation service and by OpenTargets API to the contents of the map (see here for a detailed description)
GSEA calculating gene set enrichment for the data overlays in the PD map, both publicly available and user-provided (see here for a detailed description)
Uploaded genetic variants match their protein structure
In the earlier MINERVA release we introduced handling overlays of genetic variants (if you’re interested, take a look here). Now, for the variants affecting the protein-coding regions, MINERVA links them to the structures displayed in MolArt. We have prepared a small example to illustrate this functionality. This file contains an example overlay with 42 PRKN variants, annotated by Proteins API. Take a look at the screenshot below, showing the structure of the Parkin (PRKN) dimer. Besides the regular panel of annotations available via MolArt, the dataset
MINERVA overlay - PRKN variants example is available (marked by red rectangle). Selecting it shows only the variants of this overlay and allows highlighting them. In the image below, the (C289G variant)[https://www.ncbi.nlm.nih.gov/pubmed/20889486] is selected, and its position in the PRKN structure is automatically highlighted (marked by red circles). The right panel is shown in two versions with different opacity set by the slider below the structure.
The support of SBML by MINERVA has improved, as
render packages are now handled. Exports of the PD map contents to SBML will preserve the layout of the map. We hope this will help to advance construction of detailed, mechanistic models of PD pathogenesis.
We hope you’ll enjoy the new features of MINERVA in exploring the PD map.