A Multi-Label Classification Framework to Predict Disease Associations of Long Non-coding RNAs (lncRNAs)

  • Ashis Kumer Biswas
  • Baoju Zhang
  • Xiaoyong Wu
  • Jean X. Gao
Part of the Lecture Notes in Electrical Engineering book series (LNEE, volume 322)

Abstract

In this paper, the automated detection of tissue specific disease association of long non-coding RNAs (lncRNAs) is modeled as a multi-label classification task, where a single lncRNA transcript may be associated with several diseases in a tissue specific manner. Four algorithms are evaluated and compared in this task. Furthermore, in this article we put emphasis on the fact that secondary structure and the composition features of the lncRNAs dictate their functions that led us to develop a new multi-label feature extraction scheme. Experiments are conducted on a set of 7,566 lncRNA transcripts with 22 tissue labels, and the results provide interesting insights into the quality of the discussed algorithms and the features.

Keywords

Long non-coding RNA Multi-label classification Association 

References

  1. 1.
    Sacco LD, Baldassarre A, Masotti A (2012) Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis. Int J Mol Sci 13(1):97–114Google Scholar
  2. 2.
    Liu M-X, Chen X, Chen G, Cui Q-H, Yan G-Y (2014) A computational framework to infer human disease-associated long noncoding RNAs. PLoS ONE 9(1):e84408CrossRefGoogle Scholar
  3. 3.
    Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, Zhang Q, Yan G, Cui Q (2013) LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 41(D1):D983–D986CrossRefGoogle Scholar
  4. 4.
    Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915–1927CrossRefGoogle Scholar
  5. 5.
    Mercer TR, Mattick JS (2013) Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 20(3):300–307CrossRefGoogle Scholar
  6. 6.
    Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Chem Mon 125(2):167–188CrossRefGoogle Scholar
  7. 7.
    Sato K, Hamada M, Asai K, Mituyama T (2009) CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res 37(suppl 2):W277–W280CrossRefGoogle Scholar
  8. 8.
    Tsoumakas G, Katakis I (2007) Multi-label classification: an overview. Int J Data Warehouse Min 3(3):1–13CrossRefGoogle Scholar
  9. 9.
    Santos AM, Canuto AMP, Neto AF (2011) A comparative analysis of classification methods to multi-label tasks in different application domains. Int J Comput Inf Syst Ind Manag Appl 3:218–227Google Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Ashis Kumer Biswas
    • 1
  • Baoju Zhang
    • 2
  • Xiaoyong Wu
    • 2
  • Jean X. Gao
    • 1
  1. 1.Department of Computer Science and EngineeringThe University of Texas at ArlingtonArlingtonUSA
  2. 2.School of Communications and Electronic InformationTianjin Normal UniversityTianjinChina

Personalised recommendations