A new framework for co-clustering of gene expression data

Shuzhong Zhang, Kun Wang, Bilian Chen, Xiuzhen Huang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations

Abstract

A new framework is proposed to study the co-clustering of gene expression data. This framework is based on a generic tensor optimization model and an optimization method termed Maximum Block Improvement (MBI) recently developed in [3]. Not only can this framework be applied for co-clustering gene expression data with genes expressed at different conditions represented in 2D matrices, but it can also be readily applied for co-clustering more complex high-dimensional gene expression data with genes expressed at different tissues, different development stages, different time points, different stimulations, etc. Moreover, the new framework is so flexible that it poses no difficulty at all to incorporate a variety of clustering quality measurements. In this paper, we demonstrate the effectiveness of this new approach by providing the details of one specific implementation of the algorithm, and presenting the experimental testing on microarray gene expression datasets. Our results show that the new algorithm is very efficient and it performs well for identifying patterns in gene expression datasets.

Original languageEnglish (US)
Title of host publicationPattern Recognition in Bioinformatics - 6th IAPR International Conference, PRIB 2011, Proceedings
Pages1-12
Number of pages12
DOIs
StatePublished - Nov 9 2011
Event6th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2011 - Delft, Netherlands
Duration: Nov 2 2011Nov 4 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7036 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other6th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2011
CountryNetherlands
CityDelft
Period11/2/1111/4/11

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  • Cite this

    Zhang, S., Wang, K., Chen, B., & Huang, X. (2011). A new framework for co-clustering of gene expression data. In Pattern Recognition in Bioinformatics - 6th IAPR International Conference, PRIB 2011, Proceedings (pp. 1-12). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7036 LNBI). https://doi.org/10.1007/978-3-642-24855-9_1