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Database (Oxford). 2014 Nov 7;2014. pii: bau101. doi: 10.1093/database/bau101. Print 2014.

A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools.

Author information

1
Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, GR, Greece, Department of Dermatology, University of Athens, School of Medicine, Andreas Sygros Hospital, Ι. Dragoumi 5, 161 21 Athens, GR, Greece, Department of Vertebrate Genomics, Neuropsychiatric Genetics Group, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, DE, Germany, Department of Neurology, Focus Program Translational Neuroscience, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, DE, Germany, Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, 451 10 Ioannina, GR, Greece, Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, Norfolk Place, W2 1PG, London, UK, Department of Medicine Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA, Department of Health Research and Policy, Stanford Prevention Research Center, Stanford University School of Medicine, CA, USA, Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA, USA and Department of Medicine, School of Public Health, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, UK.
2
Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, GR, Greece, Department of Dermatology, University of Athens, School of Medicine, Andreas Sygros Hospital, Ι. Dragoumi 5, 161 21 Athens, GR, Greece, Department of Vertebrate Genomics, Neuropsychiatric Genetics Group, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, DE, Germany, Department of Neurology, Focus Program Translational Neuroscience, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, DE, Germany, Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, 451 10 Ioannina, GR, Greece, Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, Norfolk Place, W2 1PG, London, UK, Department of Medicine Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA, Department of Health Research and Policy, Stanford Prevention Research Center, Stanford University School of Medicine, CA, USA, Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA, USA and Department of Medicine, School of Public Health, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, UK Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, GR, Greece, Department of Dermatology, University of Athens, School of Medicine, Andreas Sygros Hospital, Ι. Dragoumi 5, 161 21 Athens, GR, Greece, Department of Vertebrate Genomics, Neuropsychiatric Genetics Group, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, DE, Germany, Department of Neurology, Focus Program Translational Neuroscience, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, DE, Germany, Department of Hygiene and Epidemiology, Clinical and Molecular Epidemio
3
Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, GR, Greece, Department of Dermatology, University of Athens, School of Medicine, Andreas Sygros Hospital, Ι. Dragoumi 5, 161 21 Athens, GR, Greece, Department of Vertebrate Genomics, Neuropsychiatric Genetics Group, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, DE, Germany, Department of Neurology, Focus Program Translational Neuroscience, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, DE, Germany, Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, 451 10 Ioannina, GR, Greece, Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, Norfolk Place, W2 1PG, London, UK, Department of Medicine Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA, Department of Health Research and Policy, Stanford Prevention Research Center, Stanford University School of Medicine, CA, USA, Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA, USA and Department of Medicine, School of Public Health, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, UK gspyrou@bioacademy.gr.

Abstract

The publicly available online database MelGene provides a comprehensive, regularly updated, collection of data from genetic association studies in cutaneous melanoma (CM), including random-effects meta-analysis results of all eligible polymorphisms. The updated database version includes data from 192 publications with information on 1114 significantly associated polymorphisms across 280 genes, along with new front-end and back-end capabilities. Various types of relationships between data are calculated and visualized as networks. We constructed 13 different networks containing the polymorphisms and the genes included in MelGene. We explored the derived network representations under the following questions: (i) are there nodes that deserve consideration regarding their network connectivity characteristics? (ii) What is the relation of either the genome-wide or nominally significant CM polymorphisms/genes with the ones highlighted by the network representation? We show that our network approach using the MelGene data reveals connections between statistically significant genes/ polymorphisms and other genes/polymorphisms acting as 'hubs' in the reconstructed networks. To the best of our knowledge, this is the first database containing data from a comprehensive field synopsis and systematic meta-analyses of genetic polymorphisms in CM that provides user-friendly tools for in-depth molecular network visualization and exploration. The proposed network connections highlight potentially new loci requiring further investigation of their relation to melanoma risk. Database URL: http://www.melgene.org.

PMID:
25380778
PMCID:
PMC4224266
DOI:
10.1093/database/bau101
[Indexed for MEDLINE]
Free PMC Article

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