DDN: a caBIG® analytical tool for differential network analysis

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 Cent...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2011-04, Vol.27 (7), p.1036-1038
Main Authors: BAI ZHANG, YE TIAN, YUE WANG, LU JIN, HUAI LI, SHIH, Le-Ming, MADHAVAN, Subha, CLARKE, Robert, HOFFMAN, Eric P, JIANHUA XUAN, HILAKIVI-CLARKE, Leena
Format: Article
Language:English
Subjects:
Animals
Applications Note
Biological and medical sciences
Computational Biology
Epigenesis, Genetic
Female
Fundamental and applied biological sciences. Psychology
Gene Regulatory Networks
General aspects
Mammary Glands, Animal - metabolism
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Rats
Software
Systems Biology
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Summary: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. The Java and MATLAB source code can be downloaded at the authors' web site http://www.cbil.ece.vt.edu/software.htm.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btr052