TY - JOUR
T1 - A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools
AU - Athanasiadis, Emmanouil I.
AU - Antonopoulou, Kyriaki
AU - Chatzinasiou, Foteini
AU - Lill, Christina M.
AU - Bourdakou, Marilena M.
AU - Sakellariou, Argiris
AU - Kypreou, Katerina
AU - Stefanaki, Irene
AU - Evangelou, Evangelos
AU - Ioannidis, John P.A.
AU - Bertram, Lars
AU - Stratigos, Alexander J.
AU - Spyrou, George M.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84925546270&partnerID=8YFLogxK
U2 - 10.1093/database/bau101
DO - 10.1093/database/bau101
M3 - Journal articles
C2 - 25380778
AN - SCOPUS:84925546270
VL - 2014
JO - Database : the journal of biological databases and curation
JF - Database : the journal of biological databases and curation
ER -
