KDDN: An open-source Cytoscape app for constructing differential dependency networks with significant rewiring

Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie Ming Shih, Jianhua Xuan, David M. Herrington, Yue Wang

Research output: Contribution to journalArticle

Abstract

We have developed an integrated molecular network learning method, within a well-grounded mathematical framework, to construct differential dependency networks with significant rewiring. This knowledge-fused differential dependency networks (KDDN) method, implemented as a Java Cytoscape app, can be used to optimally integrate prior biological knowledge with measured data to simultaneously construct both common and differential networks, to quantitatively assign model parameters and significant rewiring p-values and to provide user-friendly graphical results. The KDDN algorithm is computationally efficient and provides users with parallel computing capability using ubiquitous multi-core machines. We demonstrate the performance of KDDN on various simulations and real gene expression datasets, and further compare the results with those obtained by the most relevant peer methods. The acquired biologically plausible results provide new insights into network rewiring as a mechanistic principle and illustrate KDDN's ability to detect them efficiently and correctly. Although the principal application here involves microarray gene expressions, our methodology can be readily applied to other types of quantitative molecular profiling data.

Original languageEnglish (US)
Pages (from-to)287-289
Number of pages3
JournalBioinformatics
Volume31
Issue number2
DOIs
StatePublished - Jan 15 2015

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Application programs
Gene expression
Open Source
Microarrays
Parallel processing systems
Gene Expression
Aptitude
Learning
Network Algorithms
p-Value
Parallel Computing
Profiling
Microarray
Java
Assign
Knowledge
Dependency (Psychology)
Integrate
Methodology
Demonstrate

ASJC Scopus subject areas

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

Cite this

KDDN : An open-source Cytoscape app for constructing differential dependency networks with significant rewiring. / Tian, Ye; Zhang, Bai; Hoffman, Eric P.; Clarke, Robert; Zhang, Zhen; Shih, Ie Ming; Xuan, Jianhua; Herrington, David M.; Wang, Yue.

In: Bioinformatics, Vol. 31, No. 2, 15.01.2015, p. 287-289.

Research output: Contribution to journalArticle

Tian, Ye ; Zhang, Bai ; Hoffman, Eric P. ; Clarke, Robert ; Zhang, Zhen ; Shih, Ie Ming ; Xuan, Jianhua ; Herrington, David M. ; Wang, Yue. / KDDN : An open-source Cytoscape app for constructing differential dependency networks with significant rewiring. In: Bioinformatics. 2015 ; Vol. 31, No. 2. pp. 287-289.
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