Deep learning for inferring gene relationships from single-cell expression data

Abstract Several methods were developed to mine gene-gene relationships from expression data. Examples include correlation and mutual information methods for co-expression analysis, clustering and undirected graphical models for functional assignments and directed graphical models for pathway reconstruction. Using a novel encoding for gene expression data, followed by deep neural networks analysis, we present a framework that can successfully address all these diverse tasks. We show that our method, CNNC, improves upon prior methods in tasks ranging from predicting transcription factor targets to identifying disease related genes to causality inference. CNNC’s encoding provides insights about some of the decisions it makes and their biological basis. CNNC is flexible and can easily be extended to integrate additional types of genomics data leading to further improvements in its performance. Supporting website with software and data: https://github.com/xiaoyeye/CNNC .