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FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development
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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000Research
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786896/ https://www.ncbi.nlm.nih.gov/pubmed/26998229 http://dx.doi.org/10.12688/f1000research.7556.1 |
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author | Koestler, Stefan A. Alaybeyoglu, Begum Weichenberger, Christian X. Celik, Arzu |
author_facet | Koestler, Stefan A. Alaybeyoglu, Begum Weichenberger, Christian X. Celik, Arzu |
author_sort | Koestler, Stefan A. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4786896 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | F1000Research |
record_format | MEDLINE/PubMed |
spelling | pubmed-47868962016-03-17 FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development Koestler, Stefan A. Alaybeyoglu, Begum Weichenberger, Christian X. Celik, Arzu F1000Res Software Tool Article 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. F1000Research 2015-12-21 /pmc/articles/PMC4786896/ /pubmed/26998229 http://dx.doi.org/10.12688/f1000research.7556.1 Text en Copyright: © 2015 Koestler SA et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Tool Article Koestler, Stefan A. Alaybeyoglu, Begum Weichenberger, Christian X. Celik, Arzu FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development |
title | FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in
Drosophila eye development |
title_full | FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in
Drosophila eye development |
title_fullStr | FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in
Drosophila eye development |
title_full_unstemmed | FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in
Drosophila eye development |
title_short | FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in
Drosophila eye development |
title_sort | flyode - a platform for community curation and interactive visualization of dynamic gene regulatory networks in
drosophila eye development |
topic | Software Tool Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786896/ https://www.ncbi.nlm.nih.gov/pubmed/26998229 http://dx.doi.org/10.12688/f1000research.7556.1 |
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