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

Athanasiadis, Emmanouil I.; Antonopoulou, Kyriaki; Chatzinasiou, Foteini; Lill, Christina M.; Bourdakou, Marilena M.; Sakellariou, Argiris; Kypreou, Katerina; Stefanaki, Irene; Evangelou, Evangelos; Ioannidis, John P.A.; Bertram, Lars; Stratigos, Alexander J.; Spyrou, George M.

doi:10.1093/database/bau101

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

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Lill, Christina M.
Neuropsychiatric Genetics (Lars Bertram), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Bertram, Lars
Neuropsychiatric Genetics (Lars Bertram), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Athanasiadis, E. I., Antonopoulou, K., Chatzinasiou, F., Lill, C. M., Bourdakou, M. M., Sakellariou, A., et al. (2014). A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools. Database: The Journal of Biological Databases and Curation, 2014: pii: bau101. doi:10.1093/database/bau101.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0026-AFF2-5

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.