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bioRxiv · 10.1101/644070

An omnidirectional visualization model of personalized gene regulatory networks

Chen, C.·Jiang, L.·Wang, M.·Wang, Y.·Shen, B.·Liu, Z.·Wang, Z.·Hou, W.·Berceli, S.·Wu, R.
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Abstract

Gene regulatory networks (GRNs) have been widely used as a fundamental tool to reveal the genomic mechanisms that underlie the organisms response to environmental and developmental cues. Standard approaches infer GRNs as holistic graphs of gene co-expression, but such graphs cannot quantify how gene-gene interactions differentiate among organisms and how they alter structurally across spatiotemporal gradients. Here, we develop a generalized framework for inferring informative, dynamic, omnidirectional, and personalized GRNs (idopGRNs) from routine transcriptional experiments. This framework is constructed by a system of quasi-dynamic ordinary differential equations (qdODEs) derived from the combination of ecological and evolutionary theories. We reconstruct idopGRNs from a clinical genomic study and illustrate how network structure and organization affect surgical response to infrainguinal vein bypass grafting and the outcome of grafting. idopGNRs may shed light on genotype-phenotype relationships and provide valuable information for personalized medicine.

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Chen, C., Jiang, L., Wang, M., Wang, Y., Shen, B., Liu, Z., Wang, Z., Hou, W., Berceli, S., Wu, R.. 2019-05-21. An omnidirectional visualization model of personalized gene regulatory networks. https://doi.org/10.1101/644070

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