title: Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview.
abstract: BACKGROUND
  DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes.
  
  
  RESULTS
  Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools.
  
  
  CONCLUSIONS
  DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.
authors.affiliation: Bioinformatics and Computational Biosciences Branch (BCBB), Office of Cyber Infrastructure and Computational Biology (OCICB), National Institute of Allergy and Infectious Disease (NIAID), National Institutes if Health (NIH), Bethesda, Maryland, USA.
authors.forename: Jeff
authors.initials: J
authors.lastname: Skinner
authors.forename: Yuri
authors.initials: Y
authors.lastname: Kotliarov
authors.forename: Sudhir
authors.initials: S
authors.lastname: Varma
authors.forename: Karina L
authors.initials: KL
authors.lastname: Mine
authors.forename: Anatoly
authors.initials: A
authors.lastname: Yambartsev
authors.forename: Richard
authors.initials: R
authors.lastname: Simon
authors.forename: Yentram
authors.initials: Y
authors.lastname: Huyen
authors.forename: Andrey
authors.initials: A
authors.lastname: Morgun
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D005910:Glioma / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software