SnvDMiR: Associating the genomic proximity of genetic variants with deregulated miRNAs and differentially methylated regions

HAMED, M and HELMS, V and ZAPP, A (2015) SnvDMiR: Associating the genomic proximity of genetic variants with deregulated miRNAs and differentially methylated regions. In: Second International Conference on Advances in Bio-Informatics and Environmental Engineering - ICABEE 2015, 18 - 19 April, 2015, Rome, Italy.

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Abstract

Although next generation sequencing of diseased traits has unraveled thousands of DNA alterations, the functional relevance of most of these mutations and how they relate to other epigenetic mechanisms are still poorly understood. Here, we present SnvDMiR as a freely–available R pipeline that conducts combinatorial proximity analysis between disease– associated SNVs, deregulated miRNAs, and differentially methylated regions (DMRs) to identify genomically adjacent SNV-miRNA pairs as well as SNV-DMR pairs. These variants could be further investigated as putative candidates for driving pathogenic processes in diseases. We demonstrated the usefulness of the SnvDMiR pipeline by applying it on a published set of breast cancer-related mutations, deregulated miRNAs, and DMRs. Our pipeline characterized potential driver mutations that are predicted to have damaging effects on related protein functions. Availability: http://gepard.bioinformatik.unisaarland. de/software

Item Type: Conference or Workshop Item (Paper)
Uncontrolled Keywords: Single Nucleotide Variant (SNV), somatic mutation, deregulated miRNA, differentially methylated region (DMR), genomic proximity, epigenetics, data integration, breast cancer.
Depositing User: Mr. John Steve
Date Deposited: 02 May 2019 11:18
Last Modified: 02 May 2019 11:18
URI: http://publications.theired.org/id/eprint/1874

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