title: DDN: a caBIG® analytical tool for differential network analysis.
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.
  
  
  BACKGROUND
  The Java and MATLAB source code can be downloaded at the authors' web site http://www.cbil.ece.vt.edu/software.htm.
authors.affiliation: Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA.
authors.forename: Bai
authors.initials: B
authors.lastname: Zhang
authors.forename: Ye
authors.initials: Y
authors.lastname: Tian
authors.forename: Lu
authors.initials: L
authors.lastname: Jin
authors.forename: Huai
authors.initials: H
authors.lastname: Li
authors.forename: Ie-Ming
authors.initials: IeM
authors.lastname: Shih
authors.forename: Subha
authors.initials: S
authors.lastname: Madhavan
authors.forename: Robert
authors.initials: R
authors.lastname: Clarke
authors.forename: Eric P
authors.initials: EP
authors.lastname: Hoffman
authors.forename: Jianhua
authors.initials: J
authors.lastname: Xuan
authors.forename: Leena
authors.initials: L
authors.lastname: Hilakivi-Clarke
authors.forename: Yue
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000818:Animals; D019295:Computational Biology; D044127:Epigenesis, Genetic; D005260:Female; D053263:Gene Regulatory Networks; D008321:Mammary Glands, Animal / Q000378:metabolism; D051381:Rats; D012984:Software; D049490:Systems Biology