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Nucleic Acids Research Advance Access originally published online on November 23, 2008
Nucleic Acids Research 2009 37(Database issue):D1001-D1005; doi:10.1093/nar/gkn905
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Nucleic Acids Research, 2009, Vol. 37, Database issue D1001-D1005
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

Update of the Diatom EST Database: a new tool for digital transcriptomics

Uma Maheswari1, Thomas Mock2, E. Virginia Armbrust2 and Chris Bowler1,3,*

1CNRS UMR8186, Department of Biology, Ecole Normale Supérieure, Paris, France, 2School of Oceanography, University of Washington, Seattle, WA 98195, USA and 3Stazione Zoologica ‘Anton Dohrn’, Villa Comunale, I-80121 Naples, Italy

*To whom correspondence should be addressed. Tel: +33 1 44323525; Fax: +33 1 44323935; Email: cbowler{at}biologie.ens.fr

Received September 15, 2008. Revised October 24, 2008. Accepted October 28, 2008.

The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130 000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77 000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3.

Present address: Thomas Mock, School of Environmental Sciences, University of East Anglia, Norwich, UK.


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V. De Riso, R. Raniello, F. Maumus, A. Rogato, C. Bowler, and A. Falciatore
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