A Database for Management of Gene Expression Data in Situ

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2004 Apr 3

PMID 15059825

Citations 56

Authors

Ekaterina Poustelnikova

Andrei Pisarev

Maxim Blagov

Maria Samsonova

John Reinitz

Affiliations

Soon will be listed here.

Abstract

Motivation: To create a spatiotemporal atlas of Drosophila segmentation gene expression at cellular resolution.

Results: The expression of segmentation genes plays a crucial role in the establishment of the Drosophila body plan. Using the IBM DB2 Relational Database Management System we have designed and implemented the FlyEx database. FlyEx contains 2832 images of 14 segmentation gene expression patterns obtained from 954 embryos and 2,073,662 quantitative data records. The averaged data is available for most of segmentation genes at eight time points. 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 estimate the variability of gene expression patterns. We also provide the capability to download data of interest.

Availability: http://urchin.spbcas.ru/flyex, http://flyex.ams.sunysb.edu/flyex

Citing Articles

Global repression by tailless during segmentation.

Masuda L, Sabino A, Reinitz J, Ramos A, Machado-Lima A, Andrioli L Dev Biol. 2023; 505:11-23.

PMID: 37879494 PMC: 10949167. DOI: 10.1016/j.ydbio.2023.09.014.

An in silico analysis of robust but fragile gene regulation links enhancer length to robustness.

Barr K, Reinitz J, Radulescu O PLoS Comput Biol. 2019; 15(11):e1007497.

PMID: 31730659 PMC: 6881076. DOI: 10.1371/journal.pcbi.1007497.

Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Species.

Wunderlich Z, Fowlkes C, Eckenrode K, Bragdon M, Abiri A, DePace A G3 (Bethesda). 2019; 9(7):2171-2182.

PMID: 31048401 PMC: 6643877. DOI: 10.1534/g3.118.200953.

Synthesizing developmental trajectories.

Villoutreix P, Anden J, Lim B, Lu H, Kevrekidis I, Singer A PLoS Comput Biol. 2017; 13(9):e1005742.

PMID: 28922353 PMC: 5619836. DOI: 10.1371/journal.pcbi.1005742.

Causality analysis detects the regulatory role of maternal effect genes in the early embryo.

Ghodsi Z, Huang X, Hassani H Genom Data. 2016; 11:20-38.

PMID: 27924281 PMC: 5129166. DOI: 10.1016/j.gdata.2016.11.013.