Ghent University Academic Bibliography

Advanced

An ensemble biclustering approach for querying gene expression compendia with experimental lists

Riet De Smet and Kathleen Marchal UGent (2011) BIOINFORMATICS. 27(14). p.1948-1956
abstract
Motivation: Query-based biclustering techniques allow interrogating a gene expression compendium with a given gene or gene list. They do so by searching for genes in the compendium that have a profile close to the average expression profile of the genes in this query-list. As it can often not be guaranteed that the genes in a long query-list will all be mutually coexpressed, it is advisable to use each gene separately as a query. This approach, however, leaves the user with a tedious post-processing of partially redundant biclustering results. The fact that for each query-gene multiple parameter settings need to be tested in order to detect the 'most optimal bicluster size' adds to the redundancy problem. Results: To aid with this post-processing, we developed an ensemble approach to be used in combination with query-based biclustering. The method relies on a specifically designed consensus matrix in which the biclustering outcomes for multiple query-genes and for different possible parameter settings are merged in a statistically robust way. Clustering of this matrix results in distinct, non-redundant consensus biclusters that maximally reflect the information contained within the original query-based biclustering results. The usefulness of the developed approach is illustrated on a biological case study in Escherichia coli.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
DISCOVERY, MODULES, ORGANIZATION, ESCHERICHIA-COLI, MICROARRAY DATA, VISUALIZATION, PROTEIN, NETWORKS, TRANSCRIPTION, FRAMEWORK
journal title
BIOINFORMATICS
Bioinformatics
volume
27
issue
14
pages
1948 - 1956
Web of Science type
Article
Web of Science id
000292554900011
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
5.468 (2011)
JCR rank
1/46 (2011)
JCR quartile
1 (2011)
ISSN
1367-4803
DOI
10.1093/bioinformatics/btr307
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1936424
handle
http://hdl.handle.net/1854/LU-1936424
date created
2011-10-27 14:17:22
date last changed
2016-12-19 15:37:50
@article{1936424,
  abstract     = {Motivation: Query-based biclustering techniques allow interrogating a gene expression compendium with a given gene or gene list. They do so by searching for genes in the compendium that have a profile close to the average expression profile of the genes in this query-list. As it can often not be guaranteed that the genes in a long query-list will all be mutually coexpressed, it is advisable to use each gene separately as a query. This approach, however, leaves the user with a tedious post-processing of partially redundant biclustering results. The fact that for each query-gene multiple parameter settings need to be tested in order to detect the 'most optimal bicluster size' adds to the redundancy problem. 

Results: To aid with this post-processing, we developed an ensemble approach to be used in combination with query-based biclustering. The method relies on a specifically designed consensus matrix in which the biclustering outcomes for multiple query-genes and for different possible parameter settings are merged in a statistically robust way. Clustering of this matrix results in distinct, non-redundant consensus biclusters that maximally reflect the information contained within the original query-based biclustering results. The usefulness of the developed approach is illustrated on a biological case study in Escherichia coli.},
  author       = {De Smet, Riet and Marchal, Kathleen},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  keyword      = {DISCOVERY,MODULES,ORGANIZATION,ESCHERICHIA-COLI,MICROARRAY DATA,VISUALIZATION,PROTEIN,NETWORKS,TRANSCRIPTION,FRAMEWORK},
  language     = {eng},
  number       = {14},
  pages        = {1948--1956},
  title        = {An ensemble biclustering approach for querying gene expression compendia with experimental lists},
  url          = {http://dx.doi.org/10.1093/bioinformatics/btr307},
  volume       = {27},
  year         = {2011},
}

Chicago
De Smet, Riet, and Kathleen Marchal. 2011. “An Ensemble Biclustering Approach for Querying Gene Expression Compendia with Experimental Lists.” Bioinformatics 27 (14): 1948–1956.
APA
De Smet, Riet, & Marchal, K. (2011). An ensemble biclustering approach for querying gene expression compendia with experimental lists. BIOINFORMATICS, 27(14), 1948–1956.
Vancouver
1.
De Smet R, Marchal K. An ensemble biclustering approach for querying gene expression compendia with experimental lists. BIOINFORMATICS. 2011;27(14):1948–56.
MLA
De Smet, Riet, and Kathleen Marchal. “An Ensemble Biclustering Approach for Querying Gene Expression Compendia with Experimental Lists.” BIOINFORMATICS 27.14 (2011): 1948–1956. Print.