Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data

  • Oliver Rübel
  • Soile V. E. Keränen
  • Mark Biggin
  • David W. Knowles
  • Gunther H. Weber
  • Hans Hagen
  • Bernd Hamann
  • E. Wes Bethel
Part of the Mathematics and Visualization book series (MATHVISUAL)


Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila TranscriptionNetwork Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular resolution. The BDTNP team visualizes and analyzes Point- Cloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and comprehensible to developers of analysis functions.We address this challenge by linking PCX and Matlab® via a dedicated interface, thereby providing biologists seamless access to advanced data analysis functions and giving bioinformatics researchers the opportunity to integrate their analysis directly into the visualization application. To demonstrate the usefulness of this approach, we computationally model parts of the expression pattern of the gene even skipped using a genetic algorithm implemented in Matlab and integrated into PCX via our Matlab interface.


Genetic Algorithm Drosophila Embryo Target Pattern Lawrence Berkeley National Laboratory Input Regulator 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Oliver Rübel
    • 1
    • 2
    • 3
  • Soile V. E. Keränen
    • 4
  • Mark Biggin
    • 4
  • David W. Knowles
    • 5
  • Gunther H. Weber
    • 6
  • Hans Hagen
    • 3
  • Bernd Hamann
    • 1
    • 2
    • 3
  • E. Wes Bethel
    • 1
  1. 1.Computational Research DivisionLawrence Berkeley National Laboratory (LBNL)BerkeleyUSA
  2. 2.Institute for Data Analysis and Visualization (IDAV), Department of Computer ScienceUniversity of California, DavisDavisUSA
  3. 3.International Research Training Group 1131Technische Universität KaiserslauternKaiserslauternGermany
  4. 4.Genomics DivisionLBNLBerkeleyUSA
  5. 5.Life Sciences DivisionLBNLBerkeleyUSA
  6. 6.Computational Research DivisionLBNLBerkeleyUSA

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