| Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. | |
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MedLine Citation:
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PMID: 18024473 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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SUMMARY: Hierarchical clustering is a widely used method for detecting clusters in genomic data. Clusters are defined by cutting branches off the dendrogram. A common but inflexible method uses a constant height cutoff value; this method exhibits suboptimal performance on complicated dendrograms. We present the Dynamic Tree Cut R package that implements novel dynamic branch cutting methods for detecting clusters in a dendrogram depending on their shape. Compared to the constant height cutoff method, our techniques offer the following advantages: (1) they are capable of identifying nested clusters; (2) they are flexible-cluster shape parameters can be tuned to suit the application at hand; (3) they are suitable for automation; and (4) they can optionally combine the advantages of hierarchical clustering and partitioning around medoids, giving better detection of outliers. We illustrate the use of these methods by applying them to protein-protein interaction network data and to a simulated gene expression data set. AVAILABILITY: The Dynamic Tree Cut method is implemented in an R package available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting. |
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Authors:
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Peter Langfelder; Bin Zhang; Steve Horvath |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural Date: 2007-11-16 |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: 24 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2008 Mar |
Date Detail:
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Created Date: 2008-02-29 Completed Date: 2008-08-08 Revised Date: 2009-11-04 |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: England |
Other Details:
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Languages: eng Pagination: 719-20 Citation Subset: IM |
Affiliation:
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Department of Human Genetics, University of California at Los Angeles, CA 90095-7088, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Cluster Analysis* Protein Binding Proteins / metabolism |
| Grant Support | |
ID/Acronym/Agency:
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1U19AI063603-01/AI/NIAID NIH HHS; 1U24NS043562-01/NS/NINDS NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Proteins |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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