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Nucleic Acids Res. 2009 Jan;37(Database issue):D1001-5. doi: 10.1093/nar/gkn905. Epub 2008 Nov 23.

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

Author information

1
CNRS UMR8186, Department of Biology, Ecole Normale Supérieure, Paris, France.

Abstract

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.

PMID:
19029140
PMCID:
PMC2686495
DOI:
10.1093/nar/gkn905
[Indexed for MEDLINE]
Free PMC Article

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