Now showing items 1-4 of 4

  • An integrated model for visualizing biclusters from gene expression data and PPI networks 

    Authors:Aladaǧ, Ahmet Emre; Erten, Cesim; Sözdinler, Melih
    Publisher and Date:(2010)
    We provide a model to integrate the visualization of biclusters extracted from gene expresion data and the underlying PPI networks. Such an integration conveys the biologically relevant interconnection between these two structures inferred from biological experiments. We model the reliabilities of the structures using directed graphs with vertex and edge weights. The resulting graphs are drawn using appropriate weighted modifications of the algorithms necessary for the layered drawings of directed ...

  • Biclustering Expression Data Based on Expanding Localized Substructures 

    Authors:Erten, Cesim; Sözdinler, Melih
    Publisher and Date:(Springer-Verlag Berlin, 2009)
    Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. We provide a method LEB (Localize-and-Extract Biclusters) which reduces the search space into local neighborhoods within the matrix by first localizing correlated structures. The localization procedure takes its roots from effective use of graph-theoretical methods applied to problems ...

  • Improving performances of suboptimal greedy iterative biclustering heuristics via localization 

    Authors:Erten, Cesim; Sözdinler, Melih
    Publisher and Date:(Oxford University Press, 2010)
    Motivation: Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. Even the simplest versions of the problem are computationally hard. Most of the proposed solutions therefore employ greedy iterative heuristics that locally optimize a suitably assigned scoring function. Methods: We provide a fast and simple pre-processing algorithm called ...

  • Reliability-Oriented bioinformatic networks visualization 

    We present our protein-protein interaction (PPI) network visualization system RobinViz (reliability-oriented bioinformatic networks visualization). Clustering the PPI network based on gene ontology (GO) annotations or biclustered gene expression data providing a clustered visualization model based on a central/peripheral duality computing layouts with algorithms specialized for interaction reliabilities represented as weights completely automated data acquisition processing are notable features ...