title: Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm.
abstract: 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.
authors.affiliation: Knowledge Discovery Group, Institute for Information Technology, National Research Council Canada, 1200 Montréal Road, Ottawa, ON K1A 0R6, Canada. alain.tchagang@nrc-cnrc.gc.ca
authors.forename: Alain B
authors.initials: AB
authors.lastname: Tchagang
authors.forename: Sieu
authors.initials: S
authors.lastname: Phan
authors.forename: Fazel
authors.initials: F
authors.lastname: Famili
authors.forename: Heather
authors.initials: H
authors.lastname: Shearer
authors.forename: Pierre
authors.initials: P
authors.lastname: Fobert
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.forename: Jitao
authors.initials: J
authors.lastname: Zou
authors.forename: Daiqing
authors.initials: D
authors.lastname: Huang
authors.forename: Adrian
authors.initials: A
authors.lastname: Cutler
authors.forename: Ziying
authors.initials: Z
authors.lastname: Liu
authors.forename: Youlian
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000465:Algorithms; D000818:Animals; D017360:Arabidopsis; D029688:Brassica napus / Q000235:genetics / Q000254:growth & development; D016000:Cluster Analysis; D018548:Cotyledon / Q000378:metabolism; D057225:Data Mining; D020869:Gene Expression Profiling; D008288:Malaria / Q000276:immunology; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis