DDN: A caBIG® analytical tool for differential network analysis

Bai Zhang, Ye Tian, Lu Jin, Huai Li, Ie Ming Shih, Subha Madhavan, Robert Clarke, Eric P. Hoffman, Jianhua Xuan, Leena Hilakivi-Clarke, Yue Wang

Research output: Contribution to journalArticle

Abstract

Differential dependency network (DDN) is a caBIG® (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG®'s In Silico Research Centers of Excellence (ISRCE) Program, DDN enables differential network analysis and provides an alternative way for defining network biomarkers predictive of phenotypes. DDN also serves as a useful systems biology tool for users across biomedical research communities to infer how genetic, epigenetic or environment variables may affect biological networks and clinical phenotypes. Besides the standalone Java application, we have also developed a Cytoscape plug-in, CytoDDN, to integrate network analysis and visualization seamlessly.

Original languageEnglish (US)
Article numberbtr052
Pages (from-to)1036-1038
Number of pages3
JournalBioinformatics
Volume27
Issue number7
DOIs
StatePublished - Apr 2011

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Informatics
Network Analysis
Electric network analysis
Cancer
Grid
Phenotype
Systems Biology
Gene Regulatory Networks
Biomarkers
Epigenomics
Computer Simulation
Biomedical Research
Neoplasms
Visualization
Research
Biological Networks
Plug-in
Java
Integrate
Alternatives

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Zhang, B., Tian, Y., Jin, L., Li, H., Shih, I. M., Madhavan, S., ... Wang, Y. (2011). DDN: A caBIG® analytical tool for differential network analysis. Bioinformatics, 27(7), 1036-1038. [btr052]. https://doi.org/10.1093/bioinformatics/btr052

DDN : A caBIG® analytical tool for differential network analysis. / Zhang, Bai; Tian, Ye; Jin, Lu; Li, Huai; Shih, Ie Ming; Madhavan, Subha; Clarke, Robert; Hoffman, Eric P.; Xuan, Jianhua; Hilakivi-Clarke, Leena; Wang, Yue.

In: Bioinformatics, Vol. 27, No. 7, btr052, 04.2011, p. 1036-1038.

Research output: Contribution to journalArticle

Zhang, B, Tian, Y, Jin, L, Li, H, Shih, IM, Madhavan, S, Clarke, R, Hoffman, EP, Xuan, J, Hilakivi-Clarke, L & Wang, Y 2011, 'DDN: A caBIG® analytical tool for differential network analysis', Bioinformatics, vol. 27, no. 7, btr052, pp. 1036-1038. https://doi.org/10.1093/bioinformatics/btr052
Zhang, Bai ; Tian, Ye ; Jin, Lu ; Li, Huai ; Shih, Ie Ming ; Madhavan, Subha ; Clarke, Robert ; Hoffman, Eric P. ; Xuan, Jianhua ; Hilakivi-Clarke, Leena ; Wang, Yue. / DDN : A caBIG® analytical tool for differential network analysis. In: Bioinformatics. 2011 ; Vol. 27, No. 7. pp. 1036-1038.
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