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dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

BACKGROUND: Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require u...

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Autores principales: Rot, Gregor, Parikh, Anup, Curk, Tomaz, Kuspa, Adam, Shaulsky, Gad, Zupan, Blaz
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2738683/
https://www.ncbi.nlm.nih.gov/pubmed/19706156
http://dx.doi.org/10.1186/1471-2105-10-265
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author Rot, Gregor
Parikh, Anup
Curk, Tomaz
Kuspa, Adam
Shaulsky, Gad
Zupan, Blaz
author_facet Rot, Gregor
Parikh, Anup
Curk, Tomaz
Kuspa, Adam
Shaulsky, Gad
Zupan, Blaz
author_sort Rot, Gregor
collection PubMed
description BACKGROUND: Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. RESULTS: We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. CONCLUSION: dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.
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spelling pubmed-27386832009-09-05 dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface Rot, Gregor Parikh, Anup Curk, Tomaz Kuspa, Adam Shaulsky, Gad Zupan, Blaz BMC Bioinformatics Software BACKGROUND: Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. RESULTS: We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. CONCLUSION: dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms. BioMed Central 2009-08-25 /pmc/articles/PMC2738683/ /pubmed/19706156 http://dx.doi.org/10.1186/1471-2105-10-265 Text en Copyright © 2009 Rot et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Rot, Gregor
Parikh, Anup
Curk, Tomaz
Kuspa, Adam
Shaulsky, Gad
Zupan, Blaz
dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
title dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
title_full dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
title_fullStr dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
title_full_unstemmed dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
title_short dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
title_sort dictyexpress: a dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2738683/
https://www.ncbi.nlm.nih.gov/pubmed/19706156
http://dx.doi.org/10.1186/1471-2105-10-265
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