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Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm
BACKGROUND: Nowadays, it is possible to collect expression levels of a set of genes from a set of biological samples during a series of time points. Such data have three dimensions: gene-sample-time (GST). Thus they are called 3D microarray gene expression data. To take advantage of the 3D data coll...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376030/ https://www.ncbi.nlm.nih.gov/pubmed/22475802 http://dx.doi.org/10.1186/1471-2105-13-54 |
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author | Tchagang, Alain B Phan, Sieu Famili, Fazel Shearer, Heather Fobert, Pierre Huang, Yi Zou, Jitao Huang, Daiqing Cutler, Adrian Liu, Ziying Pan, Youlian |
author_facet | Tchagang, Alain B Phan, Sieu Famili, Fazel Shearer, Heather Fobert, Pierre Huang, Yi Zou, Jitao Huang, Daiqing Cutler, Adrian Liu, Ziying Pan, Youlian |
author_sort | Tchagang, Alain B |
collection | PubMed |
description | BACKGROUND: Nowadays, it is possible to collect expression levels of a set of genes from a set of biological samples during a series of time points. Such data have three dimensions: gene-sample-time (GST). Thus they are called 3D microarray gene expression data. To take advantage of the 3D data collected, and to fully understand the biological knowledge hidden in the GST data, novel subspace clustering algorithms have to be developed to effectively address the biological problem in the corresponding space. RESULTS: We developed a subspace clustering algorithm called Order Preserving Triclustering (OPTricluster), for 3D short time-series data mining. OPTricluster is able to identify 3D clusters with coherent evolution from a given 3D dataset using a combinatorial approach on the sample dimension, and the order preserving (OP) concept on the time dimension. The fusion of the two methodologies allows one to study similarities and differences between samples in terms of their temporal expression profile. OPTricluster has been successfully applied to four case studies: immune response in mice infected by malaria (Plasmodium chabaudi), systemic acquired resistance in Arabidopsis thaliana, similarities and differences between inner and outer cotyledon in Brassica napus during seed development, and to Brassica napus whole seed development. These studies showed that OPTricluster is robust to noise and is able to detect the similarities and differences between biological samples. CONCLUSIONS: Our analysis showed that OPTricluster generally outperforms other well known clustering algorithms such as the TRICLUSTER, gTRICLUSTER and K-means; it is robust to noise and can effectively mine the biological knowledge hidden in the 3D short time-series gene expression data. |
format | Online Article Text |
id | pubmed-3376030 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-33760302012-06-18 Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm Tchagang, Alain B Phan, Sieu Famili, Fazel Shearer, Heather Fobert, Pierre Huang, Yi Zou, Jitao Huang, Daiqing Cutler, Adrian Liu, Ziying Pan, Youlian BMC Bioinformatics Methodology Article BACKGROUND: Nowadays, it is possible to collect expression levels of a set of genes from a set of biological samples during a series of time points. Such data have three dimensions: gene-sample-time (GST). Thus they are called 3D microarray gene expression data. To take advantage of the 3D data collected, and to fully understand the biological knowledge hidden in the GST data, novel subspace clustering algorithms have to be developed to effectively address the biological problem in the corresponding space. RESULTS: We developed a subspace clustering algorithm called Order Preserving Triclustering (OPTricluster), for 3D short time-series data mining. OPTricluster is able to identify 3D clusters with coherent evolution from a given 3D dataset using a combinatorial approach on the sample dimension, and the order preserving (OP) concept on the time dimension. The fusion of the two methodologies allows one to study similarities and differences between samples in terms of their temporal expression profile. OPTricluster has been successfully applied to four case studies: immune response in mice infected by malaria (Plasmodium chabaudi), systemic acquired resistance in Arabidopsis thaliana, similarities and differences between inner and outer cotyledon in Brassica napus during seed development, and to Brassica napus whole seed development. These studies showed that OPTricluster is robust to noise and is able to detect the similarities and differences between biological samples. CONCLUSIONS: Our analysis showed that OPTricluster generally outperforms other well known clustering algorithms such as the TRICLUSTER, gTRICLUSTER and K-means; it is robust to noise and can effectively mine the biological knowledge hidden in the 3D short time-series gene expression data. BioMed Central 2012-04-04 /pmc/articles/PMC3376030/ /pubmed/22475802 http://dx.doi.org/10.1186/1471-2105-13-54 Text en Copyright ©2012 Tchagang et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Tchagang, Alain B Phan, Sieu Famili, Fazel Shearer, Heather Fobert, Pierre Huang, Yi Zou, Jitao Huang, Daiqing Cutler, Adrian Liu, Ziying Pan, Youlian Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm |
title | Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm |
title_full | Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm |
title_fullStr | Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm |
title_full_unstemmed | Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm |
title_short | Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm |
title_sort | mining biological information from 3d short time-series gene expression data: the optricluster algorithm |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376030/ https://www.ncbi.nlm.nih.gov/pubmed/22475802 http://dx.doi.org/10.1186/1471-2105-13-54 |
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