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Nucleic Acids Research Advance Access originally published online on October 25, 2008
Nucleic Acids Research 2009 37(Database issue):D560-D566; doi:10.1093/nar/gkn717
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Nucleic Acids Research, 2009, Vol. 37, Database issue D560-D566
© 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

FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

Andrei Pisarev1, Ekaterina Poustelnikova1, Maria Samsonova1,* and John Reinitz2

1Department of Computational Biology, St. Petersburg State Polytechnical University, St. Petersburg 195251, Russia and 2Department of Applied Mathematics and Statistics and Center for Developmental Genetics, Stony Brook University, NY 11794-3600, USA

*To whom correspondence should be addressed. Tel and Fax:+7 812 5962831; Email: samson{at}spbcas.ru

Received August 8, 2008. Revised September 29, 2008. Accepted September 30, 2008.

The datasets on gene expression are the valuable source of information about the functional state of an organism. Recently, we have acquired the large dataset on expression of segmentation genes in the Drosophila blastoderm. To provide efficient access to the data, we have developed the FlyEx database (http://urchin.spbcas.ru/flyex). FlyEx contains 4716 images of 14 segmentation gene expression patterns obtained from 1579 embryos and 9 500 000 quantitative data records. Reference data are available for all segmentation genes in cycles 11–13 and all temporal classes of cycle 14A. FlyEx supports operations on images of gene expression patterns. The database can be used to examine the quality of data, analyze the dynamics of formation of segmentation gene expression domains, as well as to estimate the variability of gene expression patterns. Currently, a user is able to monitor and analyze the dynamics of formation of segmentation gene expression domains over the whole period of segment determination, that amounts to 1.5 h of development. FlyEx supports the data downloads and construction of personal reference datasets, that makes it possible to more effectively use and analyze data.


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