J Theor Biol. 2008 Mar 21;251(2):264-74. Epub 2007 Dec 4.

A new geometric biclustering algorithm based on the Hough transform for analysis of large-scale microarray data.

Source

Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong. hyzhao@ee.cityu.edu.hk

Abstract

Biclustering is an important tool in microarray analysis when only a subset of genes co-regulates in a subset of conditions. Different from standard clustering analyses, biclustering performs simultaneous classification in both gene and condition directions in a microarray data matrix. However, the biclustering problem is inherently intractable and computationally complex. In this paper, we present a new biclustering algorithm based on the geometrical viewpoint of coherent gene expression profiles. In this method, we perform pattern identification based on the Hough transform in a column-pair space. The algorithm is especially suitable for the biclustering analysis of large-scale microarray data. Our studies show that the approach can discover significant biclusters with respect to the increased noise level and regulatory complexity. Furthermore, we also test the ability of our method to locate biologically verifiable biclusters within an annotated set of genes.

PMID:: 18199458; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

Discovering biclusters in gene expression data based on high-dimensional linear geometries. [BMC Bioinformatics. 2008]
Discovering biclusters in gene expression data based on high-dimensional linear geometries.
Gan X, Liew AW, Yan H. BMC Bioinformatics. 2008 Apr 23; 9:209. Epub 2008 Apr 23.
Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization. [BMC Bioinformatics. 2008]
Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization.
Cheng KO, Law NF, Siu WC, Liew AW. BMC Bioinformatics. 2008 Apr 23; 9:210. Epub 2008 Apr 23.
Finding multiple coherent biclusters in microarray data using variable string length multiobjective genetic algorithm. [IEEE Trans Inf Technol Biomed....]
Finding multiple coherent biclusters in microarray data using variable string length multiobjective genetic algorithm.
Maulik U, Mukhopadhyay A, Bandyopadhyay S. IEEE Trans Inf Technol Biomed. 2009 Nov; 13(6):969-75. Epub 2009 Mar 16.
Review Recent patents on biclustering algorithms for gene expression data analysis. [Recent Pat DNA Gene Seq. 2011]
Review Recent patents on biclustering algorithms for gene expression data analysis.
Liew AW, Law NF, Yan H. Recent Pat DNA Gene Seq. 2011 Aug; 5(2):117-25.
Review Emergent unsupervised clustering paradigms with potential application to bioinformatics. [Front Biosci. 2008]
Review Emergent unsupervised clustering paradigms with potential application to bioinformatics.
Miller DJ, Wang Y, Kesidis G. Front Biosci. 2008 Jan 1; 13:677-90. Epub 2008 Jan 1.

See reviews... See all...

Cited by 2 PubMed Central articles

Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization. [BMC Bioinformatics. 2008]
Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization.
Cheng KO, Law NF, Siu WC, Liew AW. BMC Bioinformatics. 2008 Apr 23; 9:210. Epub 2008 Apr 23.
Discovering biclusters in gene expression data based on high-dimensional linear geometries. [BMC Bioinformatics. 2008]
Discovering biclusters in gene expression data based on high-dimensional linear geometries.
Gan X, Liew AW, Yan H. BMC Bioinformatics. 2008 Apr 23; 9:209. Epub 2008 Apr 23.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

A new geometric biclustering algorithm based on the Hough transform for analysis...
A new geometric biclustering algorithm based on the Hough transform for analysis of large-scale microarray data.
J Theor Biol. 2008 Mar 21 ;251(2):264-74. Epub 2007 Dec 4 .

PubMed
Preferential reduction of beta cells derived from Pax6-MafB pathway in MafB defi...
Preferential reduction of beta cells derived from Pax6-MafB pathway in MafB deficient mice.
Dev Biol. 2008 Feb 15 ;314(2):443-56. Epub 2007 Dec 23 .

PubMed
Mononuclear muscle cells in Drosophila ovaries revealed by GFP protein traps.
Mononuclear muscle cells in Drosophila ovaries revealed by GFP protein traps.
Dev Biol. 2008 Feb 15 ;314(2):329-40. Epub 2007 Dec 4 .

PubMed
Sites and stages of autoreactive B cell activation and regulation.
Sites and stages of autoreactive B cell activation and regulation.
Immunity. 2008 Jan ;28(1):18-28.

PubMed
Basic amino acid in the pathogenesis of caries.
Basic amino acid in the pathogenesis of caries.
Acta Stomatol Croat. 1991 ;25(2):71-6.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: