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

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.

[1]  M. Ashburner,et al.  Systematic determination of patterns of gene expression during Drosophila embryogenesis , 2002, Genome Biology.

[2]  Monte Westerfield,et al.  The Zebrafish Information Network: the zebrafish model organism database , 2005, Nucleic Acids Res..

[3]  Johannes Jaeger,et al.  A high-throughput method for quantifying gene expression data from early Drosophila embryos , 2005, Development Genes and Evolution.

[4]  John Reinitz,et al.  Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images , 2008, Fly.

[5]  John Reinitz,et al.  Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns , 2002, ISMB.

[6]  E. Wieschaus,et al.  Requirements for autosomal gene activity during precellular stages of Drosophila melanogaster. , 1988, Development.

[7]  Nobuyoshi Shimizu,et al.  MEPD: a resource for medaka gene expression patterns , 2005, Bioinform..

[8]  Janan T. Eppig,et al.  The Mouse Gene Expression Database (GXD) , 2001, Nucleic Acids Res..

[9]  B. Alberts,et al.  Studies of nuclear and cytoplasmic behaviour during the five mitotic cycles that precede gastrulation in Drosophila embryogenesis. , 1983, Journal of cell science.

[10]  John Reinitz,et al.  A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ , 2002, Silico Biol..

[11]  Prof. Dr. José A. Campos-Ortega,et al.  The Embryonic Development of Drosophila melanogaster , 1997, Springer Berlin Heidelberg.

[12]  D Kosman,et al.  Automated assay of gene expression at cellular resolution. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[13]  Maria Samsonova,et al.  Processing of natural language queries to a relational database , 2003, ISMB.

[14]  Nicholas Burton,et al.  EMAGE: a spatial database of gene expression patterns during mouse embryo development , 2005, Nucleic Acids Res..

[15]  John Reinitz,et al.  A database for management of gene expression data in situ , 2004, Bioinform..

[16]  Manu,et al.  Characterization of the Drosophila segment determination morphome. , 2008, Developmental biology.

[17]  P. Ingham The molecular genetics of embryonic pattern formation in Drosophila , 1988, Nature.

[18]  Victor B. Strelets,et al.  FlyBase: anatomical data, images and queries , 2005, Nucleic Acids Res..

[19]  John Reinitz,et al.  Registration of the expression patterns of Drosophila segmentation genes by two independent methods , 2001, Bioinform..

[20]  J. Reinitz,et al.  Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins , 1998, Development Genes and Evolution.

[21]  John Reinitz,et al.  Removal of background signal from in situ data on the expression of segmentation genes in Drosophila , 2005, Development Genes and Evolution.

[22]  Janan T. Eppig,et al.  The mouse Gene Expression Database (GXD): 2017 update , 2016, Nucleic Acids Res..

[23]  Russ B. Altman,et al.  Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO) , 2003, Bioinform..

[24]  M. Akam,et al.  The molecular basis for metameric pattern in the Drosophila embryo. , 1987, Development.