Progeny Clustering: A Method to Identify Biological Phenotypes

Simple item page
dc.citation.journalTitleScientific Reportsen_US
dc.citation.volumeNumber5en_US
dc.contributor.authorHu, Chenyue W.en_US
dc.contributor.authorKornblau, Steven M.en_US
dc.contributor.authorSlater, John H.en_US
dc.contributor.authorQutub, Amina A.en_US
dc.date.accessioned2015-11-09T18:52:17Zen_US
dc.date.available2015-11-09T18:52:17Zen_US
dc.date.issued2015en_US
dc.description.abstractEstimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset.en_US
dc.identifier.citationHu, Chenyue W., Kornblau, Steven M., Slater, John H., et al.. "Progeny Clustering: A Method to Identify Biological Phenotypes." <i>Scientific Reports,</i> 5, (2015) Nature Publishing Group: http://dx.doi.org/10.1038/srep12894.en_US
dc.identifier.doihttp://dx.doi.org/10.1038/srep12894en_US
dc.identifier.urihttps://hdl.handle.net/1911/82035en_US
dc.language.isoengen_US
dc.publisherNature Publishing Groupen_US
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the articleﾒs Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.titleProgeny Clustering: A Method to Identify Biological Phenotypesen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
srep12894.pdf
Size:
1.65 MB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Faculty Publications
Bioengineering Publications