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Bioinformation. 2012;8(13):634-8. doi: 10.6026/97320630008634. Epub 2012 Jul 6.

CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803.

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  • 1Institute for Biotechnology and Bioengineering (Laboratório Associado), Centre for Molecular and Structural Biomedicine, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.

Abstract

Synechocystis sp. PCC6803 is one of the best studied cyanobacteria and an important model organism for our understanding of photosynthesis. The early availability of its complete genome sequence initiated numerous transcriptome studies, which have generated a wealth of expression data. Analysis of the accumulated data can be a powerful tool to study transcription in a comprehensive manner and to reveal underlying regulatory mechanisms, as well as to annotate genes whose functions are yet unknown. However, use of divergent microarray platforms, as well as distributed data storage make meta-analyses of Synechocystis expression data highly challenging, especially for researchers with limited bioinformatic expertise and resources. To facilitate utilisation of the accumulated expression data for a wider research community, we have developed CyanoEXpress, a web database for interactive exploration and visualisation of transcriptional response patterns in Synechocystis. CyanoEXpress currently comprises expression data for 3073 genes and 178 environmental and genetic perturbations obtained in 31 independent studies. At present, CyanoEXpress constitutes the most comprehensive collection of expression data available for Synechocystis and can be freely accessed.

AVAILABILITY:

The database is available for free at http://cyanoexpress.sysbiolab.eu.

KEYWORDS:

Cluster; Cyanobacteria; Database; Gene expression; Meta-analysis; Microarray; PCC6803; Synechocystis sp; Transcriptome

PMID:
22829745
PMCID:
PMC3400984
DOI:
10.6026/97320630008634
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