Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox

Alessio Giacomel; Daniel Martins; Matteo Frigo; Federico Turkheimer; Steven C R Williams; Ottavia Dipasquale; Mattia Veronese

doi:10.1016/j.xpro.2022.101315

Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox

STAR Protoc. 2022 Apr 15;3(2):101315. doi: 10.1016/j.xpro.2022.101315. eCollection 2022 Jun 17.

Authors

Alessio Giacomel¹, Daniel Martins¹, Matteo Frigo^{2

3}, Federico Turkheimer¹, Steven C R Williams¹, Ottavia Dipasquale¹, Mattia Veronese^{1

4}

Affiliations

¹ Department of Neuroimaging, IoPPN, King's College London, London, UK.
² Corsmed AB, Stockholm, Sweden.
³ ATHENA Project Team, Inria Sophia Antipolis - Mediterranée, Université Côte d'Azur, Nice, France.
⁴ Department of Information Engineering, University of Padova, Padova, Italy.

Abstract

The integration of neuroimaging and transcriptomics data, Imaging Transcriptomics, is becoming increasingly popular but standardized workflows for its implementation are still lacking. We describe the Imaging Transcriptomics toolbox, a new package that implements a full imaging transcriptomics pipeline using a user-friendly, command line interface. This toolbox allows the user to identify patterns of gene expression which correlates with a specific neuroimaging phenotype and perform gene set enrichment analyses to inform the biological interpretation of the findings using up-to-date methods. For complete details on the use and execution of this protocol, please refer to Martins et al. (2021).

Keywords: Bioinformatics; Computer sciences; Health Sciences; Neuroscience; Sequence analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Neuroimaging
Phenotype
Software*
Transcriptome*
Workflow

Grants and funding

DH_/Department of Health/United Kingdom