FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development [version 1; peer review: 3 approved]

Motivation: Understanding the regulatory mechanisms governing eye development of the model organism Drosophila melanogaster (D. m.) requires structured knowledge of the involved genes and proteins, their interactions, and dynamic expression patterns. Especially the latter information is however to a...

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Bibliographic Details
Published inF1000 research Vol. 4; p. 1484
Main Authors Koestler, Stefan A, Alaybeyoglu, Begum, Weichenberger, Christian X, Celik, Arzu
Format Journal Article
LanguageEnglish
Published England Faculty of 1000 Ltd 2015
F1000Research
F1000 Research Ltd
Subjects
Bioinformatics
Cell Signaling & Trafficking Structures
Genomics
Software Tool
visualization
database
Drosophila development
protein interaction network
community annotation
gene regulatory network
web-tool
ontology
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Summary:Motivation: Understanding the regulatory mechanisms governing eye development of the model organism Drosophila melanogaster (D. m.) requires structured knowledge of the involved genes and proteins, their interactions, and dynamic expression patterns. Especially the latter information is however to a large extent scattered throughout the literature. Results: FlyOde is an online platform for the systematic assembly of data on D. m. eye development. It consists of data on eye development obtained from the literature, and a web interface for users to interactively display these data as a gene regulatory network. Our manual curation process provides high standard structured data, following a specifically designed ontology. Visualization of gene interactions provides an overview of network topology, and filtering according to user-defined expression patterns makes it a versatile tool for daily tasks, as demonstrated by usage examples. Users are encouraged to submit additional data via a simple online form.
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Equal contribution.
S.A.K. established the concept, network, annotation and ontology, performed analysis and wrote the manuscript. B.A. generated the web application. C.X.W. performed analysis and provided input during manuscript preparation. A.C. coordinated the project. All authors contributed to proofreading the manuscript and have agreed to the final content of the manuscript.
Competing interests: No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.7556.1