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Title: Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102

Abstract

Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting biological outcome of this experiment is the indication of the extent to which the phosphorus regulatory system of this cyanobacterium affects the expression of multiple genes beyond those strictly involved in phosphorus acquisition.

Authors:
 [1];  [2];  [3];  [4];  [4];  [5];  [3];  [5]
  1. Department of Independent Surveillance Assessment and Statistics, Sandia National Laboratories, Albuquerque, NM 87185-0829, USA
  2. National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA
  3. Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202, USA
  4. Department of Biomolecular Analysis and Imaging, Sandia National Laboratories, Albuquerque, NM 87185-0895, USA
  5. Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1197681
Grant/Contract Number:  
DOE DE-FG03-O1ER63148
Resource Type:
Published Article
Journal Name:
Comparative and Functional Genomics
Additional Journal Information:
Journal Name: Comparative and Functional Genomics Journal Volume: 2009; Journal ID: ISSN 1531-6912
Publisher:
Hindawi Publishing Corporation
Country of Publication:
Country unknown/Code not available
Language:
English

Citation Formats

Thomas, E. V., Phillippy, K. H., Brahamsha, B., Haaland, D. M., Timlin, J. A., Elbourne, L. D. H., Palenik, B., and Paulsen, I. T. Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102. Country unknown/Code not available: N. p., 2009. Web. doi:10.1155/2009/950171.
Thomas, E. V., Phillippy, K. H., Brahamsha, B., Haaland, D. M., Timlin, J. A., Elbourne, L. D. H., Palenik, B., & Paulsen, I. T. Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102. Country unknown/Code not available. doi:10.1155/2009/950171.
Thomas, E. V., Phillippy, K. H., Brahamsha, B., Haaland, D. M., Timlin, J. A., Elbourne, L. D. H., Palenik, B., and Paulsen, I. T. Thu . "Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102". Country unknown/Code not available. doi:10.1155/2009/950171.
@article{osti_1197681,
title = {Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102},
author = {Thomas, E. V. and Phillippy, K. H. and Brahamsha, B. and Haaland, D. M. and Timlin, J. A. and Elbourne, L. D. H. and Palenik, B. and Paulsen, I. T.},
abstractNote = {Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting biological outcome of this experiment is the indication of the extent to which the phosphorus regulatory system of this cyanobacterium affects the expression of multiple genes beyond those strictly involved in phosphorus acquisition.},
doi = {10.1155/2009/950171},
journal = {Comparative and Functional Genomics},
number = ,
volume = 2009,
place = {Country unknown/Code not available},
year = {2009},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1155/2009/950171

Citation Metrics:
Cited by: 4 works
Citation information provided by
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