Inferring gene interaction networks from ISH images via kernelized graphical models

Abstract

New bio-technologies are being developed that allow high-throughput imaging of gene expressions, where each image captures the spatial gene expression pattern of a single gene in the tissue of interest. This paper addresses the problem of automatically inferring a gene interaction network from such images. We propose a novel kernel-based graphical model learning algorithm, that is both convex and consistent. The algorithm uses multi-instance kernels to compute similarity between the expression patterns of different genes, and then minimizes the L 1 regularized Bregman divergence to estimate a sparse gene interaction network. We apply our algorithm on a large, publicly available data set of gene expression images of Drosophila embryos, where our algorithm makes novel and interesting predictions. © 2012 Springer-Verlag.