Abstract

The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex data sets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss 1) the integration of data clustering and visualization into one framework, 2) the application of data clustering to 3D gene expression data, 3) the evaluation of the number of clusters k in the context of 3D gene expression clustering, and 4) the improvement of overall analysis quality via dedicated postprocessing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.

Keywords

Bioinformatics visualization; multimodal visualization; integrating Infovis/Scivis; visual data mining; three-dimensional gene expression; data clustering; cluster visualization; gene expression pattern; temporal expression variation; gene regulation; spatial expression pattern

Published in

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2010, Volume: 7, number: 1, pages: 64-79
Publisher: IEEE COMPUTER SOC

SLU Authors

• Luengo, Cris

  • Centre for Image Analysis, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Computer Science
Bioinformatics (Computational Biology)
Genetics


Publication identifier

DOI: https://doi.org/10.1109/TCBB.2008.49

Permanent link to this page (URI)

https://res.slu.se/id/publ/60833