Spatiotemporal Visualization of Gene Expression in the Developing Mouse Brain

Abstract

Exploring and visualizing the spatiotemporal fold change of gene expression is an increasingly important challenge especially in structures as the developing brain. Focusing on the Allen Developing Mouse Brain data, we propose a visual analytic method to facilitate such exploration. We first use 3D brain atlases and developmental ontology to capture the spatial orientations of entire structures, and next use the fold changes of gene expression to weight them to denote the spatial fold changes between any given stages. We then determine the overall aggregate spatial fold change for a given gene across the entire set of stages and visualize them using 3D renderings and PCA to glean the likely directionality and gradients of gene expression. We examine the performance of the proposed method by investigating several patterns and find that they reflect the expression data. This short paper describes a portion of the larger visual analytic framework we are constructing to visualize spatiotemporal changes of gene expression in a developing brain.