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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 7, Issue 3

Issues

SNPRanker: a tool for identification and scoring of SNPs associated to target genes

Andrea Calabria
  • Corresponding author
  • Institute for Biomedical Technologies, National Research Council, via F.lli Cervi 93, 20090, Segrate (MI), http://www.itb.cnr.it Italy
  • Dept. of Informatics, Systems and Communication, University of Milano Bicocca, Viale Sarca, 336, 20126 Milano, http://www.disco.unimib.it Italy
  • Dept. of Medicine, Surgery and Dentistry, University of Milano, Via Di Rudini 8, 20142 Milano, http://www.unimi.it, Italy
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Ettore Mosca
  • Institute for Biomedical Technologies, National Research Council, via F.lli Cervi 93, 20090, Segrate (MI), http://www.itb.cnr.it Italy
  • Dept. of Informatics, Systems and Communication, University of Milano Bicocca, Viale Sarca, 336, 20126 Milano, http://www.disco.unimib.it, Italy
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Federica Viti
  • Institute for Biomedical Technologies, National Research Council, via F.lli Cervi 93, 20090, Segrate (MI), http://www.itb.cnr.it, Italy
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  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Ivan Merelli
  • Institute for Biomedical Technologies, National Research Council, via F.lli Cervi 93, 20090, Segrate (MI), http://www.itb.cnr.it, Italy
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  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Luciano Milanesi
  • 1Institute for Biomedical Technologies, National Research Council, via F.lli Cervi 93, 20090, Segrate (MI), http://www.itb.cnr.it, Italy
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  • Other articles by this author:
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2010-138

Summary

The identification of genes and SNPs involved in human diseases remains a challenge. Many public resources, databases and applications, collect biological data and perform annotations, increasing the global biological knowledge. The need of SNPs prioritization is emerging with the development of new high-throughput genotyping technologies, which allow to develop customized disease-oriented chips. Therefore, given a list of genes related to a specific biological process or disease as input, a crucial issue is finding the most relevant SNPs to analyse. The selection of these SNPs may rely on the relevant a-priori knowledge of biomolecular features characterising all the annotated SNPs and genes of the provided list. The bioinformatics approach described here allows to retrieve a ranked list of significant SNPs from a set of input genes, such as candidate genes associated with a specific disease. The system enriches the genes set by including other genes, associated to the original ones by ontological similarity evaluation. The proposed method relies on the integration of data from public resources in a vertical perspective (from genomics to systems biology data), the evaluation of features from biomolecular knowledge, the computation of partial scores for SNPs and finally their ranking, relying on their global score. Our approach has been implemented into a web based tool called SNPRanker, which is accessible through at the URL http://www.itb.cnr.it/snpranker. An interesting application of the presented system is the prioritisation of SNPs related to genes involved in specific pathologies, in order to produce custom arrays.

About the article

Published Online: 2016-10-18

Published in Print: 2010-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 7, Issue 3, Pages 331–345, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2010-138.

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© 2010 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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