Literature DB >> 14744115

ArrayExpress: a public database of gene expression data at EBI.

Philippe Rocca-Serra1, Alvis Brazma, Helen Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Sergio Contrino, Jaak Vilo, Niran Abeygunawardena, Gaurab Mukherjee, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Susanna-Assunta Sansone.   

Abstract

ArrayExpress is a public repository for microarray-based gene expression data, resulting from the implementation of the MAGE object model to ensure accurate data structuring and the MIAME standard, which defines the annotation requirements. ArrayExpress accepts data as MAGE-ML files for direct submissions or data from MIAMExpress, the MIAME compliant web-based annotation and submission tool of EBI. A team of curators supports the submission process, providing assistance in data annotation. Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress).

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Year:  2003        PMID: 14744115     DOI: 10.1016/j.crvi.2003.09.026

Source DB:  PubMed          Journal:  C R Biol        ISSN: 1631-0691            Impact factor:   1.583


  32 in total

Review 1.  Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.

Authors:  Takeshi Obayashi; Kengo Kinoshita
Journal:  J Plant Res       Date:  2010-04-10       Impact factor: 2.629

2.  PathEx: a novel multi factors based datasets selector web tool.

Authors:  Eric Bareke; Michael Pierre; Anthoula Gaigneaux; Bertrand De Meulder; Sophie Depiereux; Fabrice Berger; Naji Habra; Eric Depiereux
Journal:  BMC Bioinformatics       Date:  2010-10-22       Impact factor: 3.169

3.  Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network.

Authors:  Ulrich Harttig; Anthony J Travis; Philippe Rocca-Serra; Marten Renkema; Ben van Ommen; Heiner Boeing
Journal:  Genes Nutr       Date:  2009-04-30       Impact factor: 5.523

4.  The challenges for molecular nutrition research 2: quantification of the nutritional phenotype.

Authors:  Ben van Ommen; Jaap Keijer; Robert Kleemann; Ruan Elliott; Christian A Drevon; Harry McArdle; Mike Gibney; Michael Müller
Journal:  Genes Nutr       Date:  2008-06-25       Impact factor: 5.523

Review 5.  Bioinformatics opportunities for identification and study of medicinal plants.

Authors:  Vivekanand Sharma; Indra Neil Sarkar
Journal:  Brief Bioinform       Date:  2012-05-15       Impact factor: 11.622

6.  Cytokinin as a mediator for regulating root system architecture in response to environmental cues.

Authors:  Eswarayya Ramireddy; Ling Chang; Thomas Schmülling
Journal:  Plant Signal Behav       Date:  2014-02-07

7.  Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells.

Authors:  Michael Pierre; Benoît DeHertogh; Anthoula Gaigneaux; Bertrand DeMeulder; Fabrice Berger; Eric Bareke; Carine Michiels; Eric Depiereux
Journal:  BMC Cancer       Date:  2010-04-30       Impact factor: 4.430

8.  Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module.

Authors:  Soichi Ozaki; Yoshiyuki Ogata; Kunihiro Suda; Atsushi Kurabayashi; Tatsuya Suzuki; Naoki Yamamoto; Yoko Iijima; Taneaki Tsugane; Takashi Fujii; Chiaki Konishi; Shuji Inai; Somnuk Bunsupa; Mami Yamazaki; Daisuke Shibata; Koh Aoki
Journal:  DNA Res       Date:  2010-02-03       Impact factor: 4.458

9.  GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.

Authors:  Yao Yu; Kang Tu; Siyuan Zheng; Yun Li; Guohui Ding; Jie Ping; Pei Hao; Yixue Li
Journal:  BMC Bioinformatics       Date:  2009-08-25       Impact factor: 3.169

10.  Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

Authors:  Duccio Cavalieri; Enrica Calura; Chiara Romualdi; Emmanuela Marchi; Marijana Radonjic; Ben Van Ommen; Michael Müller
Journal:  BMC Genomics       Date:  2009-12-11       Impact factor: 3.969

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