Topological gene expression networks recapitulate brain anatomy and function

Alice Patania; Pierluigi Selvaggi; Mattia Veronese; Ottavia Dipasquale; Paul Expert; Giovanni Petri

doi:10.1162/netn_a_00094

Topological gene expression networks recapitulate brain anatomy and function

Netw Neurosci. 2019 Jul 1;3(3):744-762. doi: 10.1162/netn_a_00094. eCollection 2019.

Authors

Alice Patania¹, Pierluigi Selvaggi², Mattia Veronese², Ottavia Dipasquale², Paul Expert², Giovanni Petri³

Affiliations

¹ Network Science Institute, Indiana University, Bloomington, IN, USA.
² Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK.
³ ISI Foundation, Turin, Italy.

Abstract

Understanding how gene expression translates to and affects human behavior is one of the ultimate goals of neuroscience. In this paper, we present a pipeline based on Mapper, a topological simplification tool, to analyze gene co-expression data. We first validate the method by reproducing key results from the literature on the Allen Human Brain Atlas and the correlations between resting-state fMRI and gene co-expression maps. We then analyze a dopamine-related gene set and find that co-expression networks produced by Mapper return a structure that matches the well-known anatomy of the dopaminergic pathway. Our results suggest that network based descriptions can be a powerful tool to explore the relationships between genetic pathways and their association with brain function and its perturbation due to illness and/or pharmacological challenges.

Keywords: Allen Human Brain Atlas; Dopamine Topological Data Analysis; Mapper; fMRI; mRNA expression.