Exploring Consensus RNA Substructural Patterns Using Subgraph Mining

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

9 Scopus Citations
View graph of relations

Author(s)

  • Qingfeng Chen
  • Chaowang Lan
  • Baoshan Chen
  • Jinyan Li
  • Chengqi Zhang

Related Research Unit(s)

Detail(s)

Original languageEnglish
Pages (from-to)1134-1146
Journal / PublicationIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume14
Issue number5
Online published26 Dec 2016
Publication statusPublished - Sept 2017

Abstract

Frequently recurring RNA structural motifs play important roles in RNA folding process and interaction with other molecules. Traditional index-based and shape-based schemas are useful in modeling RNA secondary structures but ignore the structural discrepancy of individual RNA family member. Further, the in-depth analysis of underlying substructure pattern is insufficient due to varied and unnormalized substructure data. This prevents us from understanding RNAs functions and their inherent synergistic regulation networks. This article thus proposes a novel labeled graph-based algorithm RnaGraph to uncover frequently RNA substructure patterns. Attribute data and graph data are combined to characterize diverse substructures and their correlations, respectively. Further, a top-k graph pattern mining algorithm is developed to extract interesting substructure motifs by integrating frequency and similarity. The experimental results show that our methods assist in not only modelling complex RNA secondary structures but also identifying hidden but interesting RNA substructure patterns.

Research Area(s)

  • Data mining, RNA, subgraph, substructure, support

Citation Format(s)

Exploring Consensus RNA Substructural Patterns Using Subgraph Mining. / Chen, Qingfeng; Lan, Chaowang; Chen, Baoshan et al.
In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 14, No. 5, 09.2017, p. 1134-1146.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review