Journal Article

NeuroimaGene: an R package for assessing the neurological correlates of genetically regulated gene expression

Bledsoe, Xavier, Gamazon, Eric R.

2024

Overview

Background We present the NeuroimaGene resource as an R package designed to assist researchers in identifying genes and neurologic features relevant to psychiatric and neurological health. While recent studies have identified hundreds of genes as potential components of pathophysiology in neurologic and psychiatric disease, interpreting the physiological consequences of this variation is challenging. The integration of neuroimaging data with molecular findings is a step toward addressing this challenge. In addition to sharing associations with both molecular variation and clinical phenotypes, neuroimaging features are intrinsically informative of cognitive processes. NeuroimaGene provides a tool to understand how disease-associated genes relate to the intermediate structure of the brain. Results We created NeuroimaGene, a user-friendly, open access R package now available for public use. Its primary function is to identify neuroimaging derived brain features that are impacted by genetically regulated expression of user-provided genes or gene sets. This resource can be used to (1) characterize individual genes or gene sets as relevant to the structure and function of the brain, (2) identify the region(s) of the brain or body in which expression of target gene(s) is neurologically relevant, (3) impute the brain features most impacted by user-defined gene sets such as those produced by cohort level gene association studies, and (4) generate publication level, modifiable visual plots of significant findings. We demonstrate the utility of the resource by identifying neurologic correlates of stroke-associated genes derived from pre-existing analyses. Conclusions Integrating neurologic data as an intermediate phenotype in the pathway from genes to brain-based diagnostic phenotypes increases the interpretability of molecular studies and enriches our understanding of disease pathophysiology. The NeuroimaGene R package is designed to assist in this process and is publicly available for use.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Analysis / Bioinformatics / Biomedical and Life Sciences / Brain / Brain - diagnostic imaging / Brain - metabolism / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Functional anatomy / Gene expression / Gene Expression Regulation / Genes / Genomes / Genomics / Health aspects / Humans / Life Sciences / Magnetic resonance imaging / Medical imaging / Mental disorders / Microarrays / Molecular structure / Neuroimaging / Neuroimaging - methods / Neurology / Neuropsychological tests / Pathophysiology / Phenotypes / Phenotypic variations / Physiology, Pathological / Psychiatry / R (Programming language) / Software / Structure-function relationships / Transcriptomics