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Reverse Engineering Gene Regulatory Networks Using Graph Mining

  • Haodi Jiang
  • Turki TurkiEmail author
  • Sen Zhang
  • Jason T. L. WangEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10934)

Abstract

Reverse engineering gene regulatory networks (GRNs), also known as GRN inference, refers to the process of reconstructing GRNs from gene expression data. A GRN is modeled as a directed graph in which nodes represent genes and edges show regulatory relationships between the genes. By predicting the edges to infer a GRN, biologists can gain a better understanding of regulatory circuits and functional elements in cells. Many bioinformatics tools have been developed to computationally reverse engineer GRNs. However, none of these tools is able to perform perfect GRN inference. In this paper, we propose a graph mining approach capable of discovering frequent patterns from the GRNs inferred by existing methods. These frequent or common patterns are more likely to occur in true regulatory networks. Experimental results on different datasets demonstrate the good quality of the discovered patterns, and the superiority of our approach over the existing GRN inference methods.

Keywords

Graph mining Network inference Pattern discovery Applications in biology and medicine 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Bioinformatics Program and Department of Computer Science, New Jersey Institute of TechnologyUniversity HeightsNewarkUSA
  2. 2.Computer Science DepartmentKing Abdulaziz UniversityJeddahSaudi Arabia
  3. 3.Department of Mathematics, Computer Science and StatisticsState University of New York (SUNY) College at OneontaOneontaUSA

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