| Merging microarray cell synchronization experiments through curve alignment. | |
| | |
MedLine Citation:
|
PMID: 17237107 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
MOTIVATION: The validity of periodic cell cycle regulation studies in plants is seriously compromised by the relatively poor quality of cell synchrony that is achieved for plant suspension cultures in comparison to yeast and mammals. The present state-of-the-art plant synchronization techniques cannot offer a complete cell cycle coverage and moreover a considerable loss of cell synchrony may occur toward the end of the sampling. One possible solution is to consider combining multiple datasets, produced by different synchronization techniques and thus covering different phases of the cell cycle, in order to arrive at a better cell cycle coverage. RESULTS: We propose a method that enables pasting expression profiles from different plant cell synchronization experiments and results in an expression curve that spans more than one cell cycle. The optimal pasting overlap is determined via a dynamic time warping alignment. Consequently, the different expression time series are merged together by aggregating the corresponding expression values lying within the overlap area. We demonstrate that the periodic analysis of the merged expression profiles produces more reliable p-values for periodicity. Subsequent Gene Ontology analysis of the results confirms that merging synchronization experiments is a more robust strategy for the selection of potentially periodic genes. Additional validation of the proposed algorithm on yeast data is also presented. AVAILABILITY: Results, benchmark sets and scripts are freely available at our website: http://www.psb.ugent.be/cbd/publications.php |
| | |
Authors:
|
Filip Hermans; Elena Tsiporkova |
Related Documents
:
|
11999577 - Cell cycle retardation in monocytoid cells induced by aminopeptidase n (cd13). 11302687 - Cell cycle regulation of nf-kappa b-binding activity in cells from human glioblastomas. 2567547 - Cell cycle of normal bladder urothelium in developing and adult mice. 16828087 - Cell expression of a four extra octarepeat mutated prpc modifies cell structure and cel... 22458237 - Ovarian folliculogenesis in collared peccary, pecari tajacu (artiodactyla: tayassuidae). 22447287 - Apoptosis induced by 7-difluoromethoxyl-5,4'-di-n-octyl genistein via the inactivation ... |
Publication Detail:
|
Type: Evaluation Studies; Journal Article |
Journal Detail:
|
Title: Bioinformatics (Oxford, England) Volume: 23 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2007 Jan |
Date Detail:
|
Created Date: 2007-01-22 Completed Date: 2007-03-06 Revised Date: 2009-11-04 |
Medline Journal Info:
|
Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: England |
Other Details:
|
Languages: eng Pagination: e64-70 Citation Subset: IM |
Affiliation:
|
Computational Biology Division, Department of Plant Systems Biology Flanders Institute for Biotechnology, Technologiepark 917, 9052 Ghent, Belgium. fiher@psb.ugent.be |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Algorithms* Arabidopsis / cytology*, genetics, metabolism* Arabidopsis Proteins / genetics, metabolism* Cell Cycle / physiology* Cell Cycle Proteins / metabolism* Computer Simulation Gene Expression Profiling / methods Information Storage and Retrieval / methods Models, Biological Numerical Analysis, Computer-Assisted Oligonucleotide Array Sequence Analysis / methods* |
| Chemical | |
Reg. No./Substance:
|
0/Arabidopsis Proteins; 0/Cell Cycle Proteins |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Genetic code symmetry and efficient design of GC-constrained coding sequences.
Next Document: Family relationships: should consensus reign?--consensus clustering for protein families.