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

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.
 [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:
OSTI Identifier:
Grant/Contract Number:
DOE DE-FG03-O1ER63148
Published Article
Journal Name:
Comparative and Functional Genomics
Additional Journal Information:
Journal Volume: 2009; Related Information: CHORUS Timestamp: 2016-08-11 14:01:40; Journal ID: ISSN 1531-6912
Hindawi Publishing Corporation
Sponsoring Org:
Country of Publication:
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