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Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

Authors:

Gunther H. Weber,

Mark D. Biggin,

Charless C. Fowlkes,

Cris L. Luengo Hendriks,

Soile V. E. Keranen,

Michael B. Eisen,

David W. Knowles,

Jitendra Malik,

Bernd HamannAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 7, Issue 1

Pages 64 - 79

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

Published: 01 January 2010 Publication History

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.

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Cited By

Shen QXu TLiang YChen YHe Z(2024)Robust Tensor Recovery for Incomplete Multi-View ClusteringIEEE Transactions on Multimedia10.1109/TMM.2023.332149926(3856-3870)Online publication date: 1-Jan-2024
https://dl.acm.org/doi/10.1109/TMM.2023.3321499
Turkay CParulek JHauser HLindstaedt SGranitzer M(2012)Dual analysis of DNA microarraysProceedings of the 12th International Conference on Knowledge Management and Knowledge Technologies10.1145/2362456.2362489(1-8)Online publication date: 5-Sep-2012
https://dl.acm.org/doi/10.1145/2362456.2362489
Stegmayer GMilone DKamenetzky LLopez MCarrari F(2012)A Biologically Inspired Validity Measure for Comparison of Clustering Methods over Metabolic Data SetsIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2012.109:3(706-716)Online publication date: 1-May-2012
https://dl.acm.org/doi/10.1109/TCBB.2012.10
Show More Cited By

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Machine learning
    1. Learning paradigms
      1. Unsupervised learning

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cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 7, Issue 1

January 2010

190 pages

ISSN:1545-5963

Issue’s Table of Contents

Publisher

IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 January 2010

Published in TCBB Volume 7, Issue 1

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Cited By

Shen QXu TLiang YChen YHe Z(2024)Robust Tensor Recovery for Incomplete Multi-View ClusteringIEEE Transactions on Multimedia10.1109/TMM.2023.332149926(3856-3870)Online publication date: 1-Jan-2024
https://dl.acm.org/doi/10.1109/TMM.2023.3321499
Turkay CParulek JHauser HLindstaedt SGranitzer M(2012)Dual analysis of DNA microarraysProceedings of the 12th International Conference on Knowledge Management and Knowledge Technologies10.1145/2362456.2362489(1-8)Online publication date: 5-Sep-2012
https://dl.acm.org/doi/10.1145/2362456.2362489
Stegmayer GMilone DKamenetzky LLopez MCarrari F(2012)A Biologically Inspired Validity Measure for Comparison of Clustering Methods over Metabolic Data SetsIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2012.109:3(706-716)Online publication date: 1-May-2012
https://dl.acm.org/doi/10.1109/TCBB.2012.10
Turkay CParulek JReuter NHauser HNishita T(2011)Integrating cluster formation and cluster evaluation in interactive visual analysisProceedings of the 27th Spring Conference on Computer Graphics10.1145/2461217.2461234(77-86)Online publication date: 28-Apr-2011
https://dl.acm.org/doi/10.1145/2461217.2461234
Turkay CParulek JReuter NHauser H(2011)Interactive visual analysis of temporal cluster structuresProceedings of the 13th Eurographics / IEEE - VGTC conference on Visualization10.1111/j.1467-8659.2011.01920.x(711-720)Online publication date: 1-Jun-2011
https://dl.acm.org/doi/10.1111/j.1467-8659.2011.01920.x

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