BMRF-Net: A software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method

Xu Shi, Robert O. Barnes, Li Chen, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke, Yue Wang, Jianhua Xuan

Research output: Contribution to journalArticle

Abstract

Summary: Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein-protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence.

Original languageEnglish (US)
Pages (from-to)2412-2414
Number of pages3
JournalBioinformatics
Volume31
Issue number14
DOIs
StatePublished - 2015

Fingerprint

Bagging
Software Tools
Random Field
Software
Proteins
Protein
Breast Cancer
Interaction
Breast Neoplasms
Protein-protein Interaction
Plug-in
Gene Expression Data
C++
Gene expression
Recurrence
User Interface
User interfaces
Java
Cancer
Gene Expression

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

Shi, X., Barnes, R. O., Chen, L., Shajahan-Haq, A. N., Hilakivi-Clarke, L., Clarke, R., ... Xuan, J. (2015). BMRF-Net: A software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. Bioinformatics, 31(14), 2412-2414. https://doi.org/10.1093/bioinformatics/btv137

BMRF-Net : A software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. / Shi, Xu; Barnes, Robert O.; Chen, Li; Shajahan-Haq, Ayesha N.; Hilakivi-Clarke, Leena; Clarke, Robert; Wang, Yue; Xuan, Jianhua.

In: Bioinformatics, Vol. 31, No. 14, 2015, p. 2412-2414.

Research output: Contribution to journalArticle

Shi, X, Barnes, RO, Chen, L, Shajahan-Haq, AN, Hilakivi-Clarke, L, Clarke, R, Wang, Y & Xuan, J 2015, 'BMRF-Net: A software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method', Bioinformatics, vol. 31, no. 14, pp. 2412-2414. https://doi.org/10.1093/bioinformatics/btv137
Shi, Xu ; Barnes, Robert O. ; Chen, Li ; Shajahan-Haq, Ayesha N. ; Hilakivi-Clarke, Leena ; Clarke, Robert ; Wang, Yue ; Xuan, Jianhua. / BMRF-Net : A software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. In: Bioinformatics. 2015 ; Vol. 31, No. 14. pp. 2412-2414.
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