SignatureClust

A tool for landmark gene-guided clustering

Pankaj Chopra, Hanjun Shin, Jaewoo Kang, Sunwon Lee

Research output: Contribution to journalArticle

Abstract

Over the last several years, many clustering algorithms have been applied to gene expression data. However, most clustering algorithms force the user into having one set of clusters, resulting in a restrictive biological interpretation of gene function. It would be difficult to interpret the complex biological regulatory mechanisms and genetic interactions from this restrictive interpretation of microarray expression data. The software package SignatureClust allows users to select a group of functionally related genes (called 'Landmark Genes'), and to project the gene expression data onto these genes. Compared to existing algorithms and software in this domain, our software package offers two unique benefits. First, by selecting different sets of landmark genes, it enables the user to cluster the microarray data from multiple biological perspectives. This encourages data exploration and discovery of new gene associations. Second, most packages associated with clustering provide internal validation measures, whereas our package validates the biological significance of the new clusters by retrieving significant ontology and pathway terms associated with the new clusters. SignatureClust is a free software tool that enables biologists to get multiple views of the microarray data. It highlights new gene associations that were not found using a traditional clustering algorithm. The software package 'SignatureClust' and the user manual can be downloaded from http://infos.korea.ac.kr/sigclust.php.

Original languageEnglish
Pages (from-to)411-418
Number of pages8
JournalSoft Computing
Volume16
Issue number3
DOIs
Publication statusPublished - 2012 Mar 1

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Landmarks
Genes
Clustering
Gene
Microarrays
Clustering algorithms
Software Package
Software packages
Clustering Algorithm
Gene Expression Data
Microarray Data
Gene expression
Software Tools
Microarray
Ontology
Pathway
Internal
Software
Term
Interaction

ASJC Scopus subject areas

  • Software
  • Geometry and Topology
  • Theoretical Computer Science

Cite this

SignatureClust : A tool for landmark gene-guided clustering. / Chopra, Pankaj; Shin, Hanjun; Kang, Jaewoo; Lee, Sunwon.

In: Soft Computing, Vol. 16, No. 3, 01.03.2012, p. 411-418.

Research output: Contribution to journalArticle

Chopra, Pankaj ; Shin, Hanjun ; Kang, Jaewoo ; Lee, Sunwon. / SignatureClust : A tool for landmark gene-guided clustering. In: Soft Computing. 2012 ; Vol. 16, No. 3. pp. 411-418.
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