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CORNET: a user-friendly tool for data mining and integration

Stefanie De Bodt UGent, Diana Angelica Carvajal Bernal UGent, Jens Hollunder UGent, Joost Van den Cruyce UGent, Sara Movahedi UGent and Dirk Inzé UGent (2010) PLANT PHYSIOLOGY. 152(3). p.1167-1179
abstract
As an overwhelming amount of functional genomics data have been generated, the retrieval, integration, and interpretation of these data need to be facilitated to enable the advance of (systems) biological research. For example, gathering and processing microarray data that are related to a particular biological process is not straightforward, nor is the compilation of protein-protein interactions from numerous partially overlapping databases identified through diverse approaches. However, these tasks are inevitable to address the following questions. Does a group of differentially expressed genes show similar expression in diverse microarray experiments? Was an identified protein-protein interaction previously detected by other approaches? Are the interacting proteins encoded by genes with similar expression profiles and localization? We developed CORNET (for CORrelation NETworks) as an access point to transcriptome, protein interactome, and localization data and functional information on Arabidopsis (Arabidopsis thaliana). It consists of two flexible and versatile tools, namely the coexpression tool and the protein-protein interaction tool. The ability to browse and search microarray experiments using ontology terms and the incorporation of personal microarray data are distinctive features of the microarray repository. The coexpression tool enables either the alternate or simultaneous use of diverse expression compendia, whereas the protein-protein interaction tool searches experimentally and computationally identified protein-protein interactions. Different search options are implemented to enable the construction of coexpression and/or protein-protein interaction networks centered around multiple input genes or proteins. Moreover, networks and associated evidence are visualized in Cytoscape. Localization is visualized in pie charts, thereby allowing multiple localizations per protein. CORNET is available at http://bioinformatics.psb.ugent.be/cornet
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
HYPOTHESIS GENERATION, MITOCHONDRIAL PROTEINS, SUBCELLULAR-LOCALIZATION, TERMINAL TARGETING SEQUENCES, ARABIDOPSIS-THALIANA DEVELOPMENT, FLORAL DEVELOPMENT, MODEL DATA-ANALYSIS, SEED-GERMINATION, PLANT BIOLOGY, EXPRESSION DATA
journal title
PLANT PHYSIOLOGY
Plant Physiol.
volume
152
issue
3
pages
13 pages
Web of Science type
Article
Web of Science id
000276329500005
JCR category
PLANT SCIENCES
JCR impact factor
6.451 (2010)
JCR rank
8/185 (2010)
JCR quartile
1 (2010)
ISSN
0032-0889
DOI
10.1104/pp.109.147215
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
947380
handle
http://hdl.handle.net/1854/LU-947380
date created
2010-05-17 18:24:54
date last changed
2012-09-19 14:03:44
@article{947380,
  abstract     = {As an overwhelming amount of functional genomics data have been generated, the retrieval, integration, and interpretation of these data need to be facilitated to enable the advance of (systems) biological research. For example, gathering and processing microarray data that are related to a particular biological process is not straightforward, nor is the compilation of protein-protein interactions from numerous partially overlapping databases identified through diverse approaches. However, these tasks are inevitable to address the following questions. Does a group of differentially expressed genes show similar expression in diverse microarray experiments? Was an identified protein-protein interaction previously detected by other approaches? Are the interacting proteins encoded by genes with similar expression profiles and localization? We developed CORNET (for CORrelation NETworks) as an access point to transcriptome, protein interactome, and localization data and functional information on Arabidopsis (Arabidopsis thaliana). It consists of two flexible and versatile tools, namely the coexpression tool and the protein-protein interaction tool. The ability to browse and search microarray experiments using ontology terms and the incorporation of personal microarray data are distinctive features of the microarray repository. The coexpression tool enables either the alternate or simultaneous use of diverse expression compendia, whereas the protein-protein interaction tool searches experimentally and computationally identified protein-protein interactions. Different search options are implemented to enable the construction of coexpression and/or protein-protein interaction networks centered around multiple input genes or proteins. Moreover, networks and associated evidence are visualized in Cytoscape. Localization is visualized in pie charts, thereby allowing multiple localizations per protein. CORNET is available at http://bioinformatics.psb.ugent.be/cornet},
  author       = {De Bodt, Stefanie and Carvajal Bernal, Diana Angelica and Hollunder, Jens and Van den Cruyce, Joost and Movahedi, Sara and Inz{\'e}, Dirk},
  issn         = {0032-0889},
  journal      = {PLANT PHYSIOLOGY},
  keyword      = {HYPOTHESIS GENERATION,MITOCHONDRIAL PROTEINS,SUBCELLULAR-LOCALIZATION,TERMINAL TARGETING SEQUENCES,ARABIDOPSIS-THALIANA DEVELOPMENT,FLORAL DEVELOPMENT,MODEL DATA-ANALYSIS,SEED-GERMINATION,PLANT BIOLOGY,EXPRESSION DATA},
  language     = {eng},
  number       = {3},
  pages        = {1167--1179},
  title        = {CORNET: a user-friendly tool for data mining and integration},
  url          = {http://dx.doi.org/10.1104/pp.109.147215},
  volume       = {152},
  year         = {2010},
}

Chicago
De Bodt, Stefanie, Diana Angelica Carvajal Bernal, Jens Hollunder, Joost Van den Cruyce, Sara Movahedi, and Dirk Inzé. 2010. “CORNET: a User-friendly Tool for Data Mining and Integration.” Plant Physiology 152 (3): 1167–1179.
APA
De Bodt, S., Carvajal Bernal, D. A., Hollunder, J., Van den Cruyce, J., Movahedi, S., & Inzé, D. (2010). CORNET: a user-friendly tool for data mining and integration. PLANT PHYSIOLOGY, 152(3), 1167–1179.
Vancouver
1.
De Bodt S, Carvajal Bernal DA, Hollunder J, Van den Cruyce J, Movahedi S, Inzé D. CORNET: a user-friendly tool for data mining and integration. PLANT PHYSIOLOGY. 2010;152(3):1167–79.
MLA
De Bodt, Stefanie, Diana Angelica Carvajal Bernal, Jens Hollunder, et al. “CORNET: a User-friendly Tool for Data Mining and Integration.” PLANT PHYSIOLOGY 152.3 (2010): 1167–1179. Print.