Abstract:
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Gene co-expression networks are widely used to understand gene regulations and infer gene functions, but only capture genes that express simultaneously thereby failing to describe the directed associations between genes, which are of great scientific interest. Recent advances in single-cell sequencing technology allow for the sequencing of cells individually and several algorithms now exist that can sort these cells into their pseudotemporal ordering based on gene expression. By ordering single-cell sequencing data based on sets of genes that have experimentally validated involvement in cell cycle processes, we create a pseudotime-series out of the expression profiles of individual cells. We present a time-series inspired lag-based correlation analysis of these pseudotime-series. We find significant evidence of directed associations within expression profiles from mouse samples that would be missed by traditional co-expression techniques. We confirm those associations within experimentally validated networks, as well as identify new directed associations for experimental exploration.
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