LaminaRGeneVis: A Tool to Visualize Gene Expression Across the Laminar Architecture of the Human Neocortex

Ethan H Kim; Derek Howard; Yuxiao Chen; Shreejoy J Tripathy; Leon French

doi:10.3389/fninf.2022.753770

LaminaRGeneVis: A Tool to Visualize Gene Expression Across the Laminar Architecture of the Human Neocortex

Front Neuroinform. 2022 Feb 24:16:753770. doi: 10.3389/fninf.2022.753770. eCollection 2022.

Authors

Ethan H Kim^{1

2}, Derek Howard¹, Yuxiao Chen¹, Shreejoy J Tripathy^{1

2

3}, Leon French^{1

3

4}

Affiliations

¹ Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada.
² Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
³ Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
⁴ Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada.

Abstract

The application of RNA sequencing has enabled the characterization of genome-wide gene expression in the human brain, including distinct layers of the neocortex. Neuroanatomically, the molecular patterns that underlie the laminar organization of the neocortex can help link structure to circuitry and function. To advance our understanding of cortical architecture, we created LaminaRGeneVis, a web application that displays across-layer cortical gene expression from multiple datasets. These datasets were collected using bulk, single-nucleus, and spatial RNA sequencing methodologies and were normalized to facilitate comparisons between datasets. The online resource performs single- and multi-gene analyses to provide figures and statistics for user-friendly assessment of laminar gene expression patterns in the adult human neocortex. The web application is available at https://ethanhkim.shinyapps.io/laminargenevis/.

Keywords: application (app); human brain (cerebral cortex); neocortex; neuroinformatics; transcriptomics.