Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias.

IScience
N. VavourakiClaudia Manzoni

Abstract

The Hereditary Spastic Paraplegias are a group of neurodegenerative diseases characterized by spasticity and weakness in the lower body. Owing to the combination of genetic diversity and variable clinical presentation, the Hereditary Spastic Paraplegias are a strong candidate for protein-protein interaction network analysis as a tool to understand disease mechanism(s) and to aid functional stratification of phenotypes. In this study, experimentally validated human data were used to create a protein-protein interaction network based on the causative genes. Network evaluation as a combination of topological analysis and functional annotation led to the identification of core proteins in putative shared biological processes, such as intracellular transport and vesicle trafficking. The application of machine learning techniques suggested a functional dichotomy linked with distinct sets of clinical presentations, indicating that there is scope to further classify conditions currently described under the same umbrella-term of Hereditary Spastic Paraplegias based on specific molecular mechanisms of disease.

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Citations

May 23, 2021·Neurobiology of Disease·James E Tomkins, Claudia Manzoni

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Software Mentioned

PINOT
: Profiler
R stats package
PathwayBrowser
Reactome
Cytoscape
R
R package “ pvclust ”
Panther
Profiler

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