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EuroDia : a beta-cell gene expression resource.

Liechti, Robin ; Csárdi, Gábor ; Bergmann, Sven ; Schütz, Frédéric ; Sengstag, Thierry ; Boj, Sylvia F. ; Servitja, Joan Marc ; Ferrer, Jorge ; Van Lommel, Leentje and Schuit, Frans , et al. (2010) In Database : the journal of biological databases and curation 2010.
Abstract

Type 2 diabetes mellitus (T2DM) is a major disease affecting nearly 280 million people worldwide. Whilst the pathophysiological mechanisms leading to disease are poorly understood, dysfunction of the insulin-producing pancreatic beta-cells is key event for disease development. Monitoring the gene expression profiles of pancreatic beta-cells under several genetic or chemical perturbations has shed light on genes and pathways involved in T2DM. The EuroDia database has been established to build a unique collection of gene expression measurements performed on beta-cells of three organisms, namely human, mouse and rat. The Gene Expression Data Analysis Interface (GEDAI) has been developed to support this database. The quality of each dataset... (More)

Type 2 diabetes mellitus (T2DM) is a major disease affecting nearly 280 million people worldwide. Whilst the pathophysiological mechanisms leading to disease are poorly understood, dysfunction of the insulin-producing pancreatic beta-cells is key event for disease development. Monitoring the gene expression profiles of pancreatic beta-cells under several genetic or chemical perturbations has shed light on genes and pathways involved in T2DM. The EuroDia database has been established to build a unique collection of gene expression measurements performed on beta-cells of three organisms, namely human, mouse and rat. The Gene Expression Data Analysis Interface (GEDAI) has been developed to support this database. The quality of each dataset is assessed by a series of quality control procedures to detect putative hybridization outliers. The system integrates a web interface to several standard analysis functions from R/Bioconductor to identify differentially expressed genes and pathways. It also allows the combination of multiple experiments performed on different array platforms of the same technology. The design of this system enables each user to rapidly design a custom analysis pipeline and thus produce their own list of genes and pathways. Raw and normalized data can be downloaded for each experiment. The flexible engine of this database (GEDAI) is currently used to handle gene expression data from several laboratory-run projects dealing with different organisms and platforms. Database URL: http://eurodia.vital-it.ch.

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type
Contribution to journal
publication status
published
subject
in
Database : the journal of biological databases and curation
volume
2010
publisher
Oxford University Press
external identifiers
  • scopus:79952047616
  • pmid:20940178
ISSN
1758-0463
DOI
10.1093/database/baq024
language
English
LU publication?
yes
id
84ecc4e4-6de4-48b1-8f7f-908d6c9e843d
date added to LUP
2018-10-01 13:48:04
date last changed
2021-04-06 04:56:20
@article{84ecc4e4-6de4-48b1-8f7f-908d6c9e843d,
  abstract     = {<p>Type 2 diabetes mellitus (T2DM) is a major disease affecting nearly 280 million people worldwide. Whilst the pathophysiological mechanisms leading to disease are poorly understood, dysfunction of the insulin-producing pancreatic beta-cells is key event for disease development. Monitoring the gene expression profiles of pancreatic beta-cells under several genetic or chemical perturbations has shed light on genes and pathways involved in T2DM. The EuroDia database has been established to build a unique collection of gene expression measurements performed on beta-cells of three organisms, namely human, mouse and rat. The Gene Expression Data Analysis Interface (GEDAI) has been developed to support this database. The quality of each dataset is assessed by a series of quality control procedures to detect putative hybridization outliers. The system integrates a web interface to several standard analysis functions from R/Bioconductor to identify differentially expressed genes and pathways. It also allows the combination of multiple experiments performed on different array platforms of the same technology. The design of this system enables each user to rapidly design a custom analysis pipeline and thus produce their own list of genes and pathways. Raw and normalized data can be downloaded for each experiment. The flexible engine of this database (GEDAI) is currently used to handle gene expression data from several laboratory-run projects dealing with different organisms and platforms. Database URL: http://eurodia.vital-it.ch.</p>},
  author       = {Liechti, Robin and Csárdi, Gábor and Bergmann, Sven and Schütz, Frédéric and Sengstag, Thierry and Boj, Sylvia F. and Servitja, Joan Marc and Ferrer, Jorge and Van Lommel, Leentje and Schuit, Frans and Klinger, Sonia and Thorens, Bernard and Naamane, Najib and Eizirik, Decio L. and Marselli, Lorella and Bugliani, Marco and Marchetti, Piero and Lucas, Stephanie and Holm, Cecilia and Jongeneel, C. Victor and Xenarios, Ioannis},
  issn         = {1758-0463},
  language     = {eng},
  month        = {01},
  publisher    = {Oxford University Press},
  series       = {Database : the journal of biological databases and curation},
  title        = {EuroDia : a beta-cell gene expression resource.},
  url          = {http://dx.doi.org/10.1093/database/baq024},
  doi          = {10.1093/database/baq024},
  volume       = {2010},
  year         = {2010},
}