Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses?

Marzena Dolbniak; Joanna Zyla; Sylwia Kabacik; Grainne Manning; Christophe Badie; Ghazi Alsbeih; Joanna Polanska

doi:10.5220/0005286102430250

Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses?

Marzena Dolbniak, Joanna Zyla, Sylwia Kabacik, Grainne Manning, Christophe Badie, Ghazi Alsbeih, Joanna Polanska

HP: Radiation Effects

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Genome-Wide Association Studies (GWAS) are of great importance in identifying the genetic variants associated with traits/diseases. Due to the high number of candidate SNPs some filtering techniques are necessary to be applied. The aim of the study was to develop the comprehensive approach allowing for detailed analysis of both SNP-gene and SNP-miRNA-gene relations. We elaborated and optimized the novel signal analysis pipeline improving significantly the results of the analysis on genotype-phenotype interplay. Direct links between genotype results and gene expression levels were enriched by detailed analysis of SNP-miRNA-gene interactions at both mature miRNA structure/seed region and target binding site level. The proposed technique was applied to the data on lymphocyte radiation response and increased by almost 100% number of potential functional SNPs.

Original language	English
Title of host publication	BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015
Editors	Oscar Pastor, Christine Sinoquet, Ana Fred, Hugo Gamboa, Dirk Elias
Publisher	SciTePress
Pages	243-250
Number of pages	8
ISBN (Electronic)	9789897580703
DOIs	https://doi.org/10.5220/0005286102430250
Publication status	Published - 2015
Event	6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015 - Lisbon, Portugal Duration: 12 Jan 2015 → 15 Jan 2015

Publication series

Name	BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015

Conference

Conference	6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015
Country/Territory	Portugal
City	Lisbon
Period	12/01/15 → 15/01/15

Keywords

GWAS
Gene expression
Radiation
Radiosensitivity
Single nucleotide polymorphism
miRNA

Access to Document

10.5220/0005286102430250

Cite this

Dolbniak, M., Zyla, J., Kabacik, S., Manning, G., Badie, C., Alsbeih, G., & Polanska, J. (2015). Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses? In O. Pastor, C. Sinoquet, A. Fred, H. Gamboa, & D. Elias (Eds.), BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015 (pp. 243-250). (BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015). SciTePress. https://doi.org/10.5220/0005286102430250

Dolbniak, Marzena ; Zyla, Joanna ; Kabacik, Sylwia et al. / Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses?. BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015. editor / Oscar Pastor ; Christine Sinoquet ; Ana Fred ; Hugo Gamboa ; Dirk Elias. SciTePress, 2015. pp. 243-250 (BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015).

@inproceedings{e31bf3ec3d004292accfc06c3726060e,

title = "Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses?",

abstract = "Genome-Wide Association Studies (GWAS) are of great importance in identifying the genetic variants associated with traits/diseases. Due to the high number of candidate SNPs some filtering techniques are necessary to be applied. The aim of the study was to develop the comprehensive approach allowing for detailed analysis of both SNP-gene and SNP-miRNA-gene relations. We elaborated and optimized the novel signal analysis pipeline improving significantly the results of the analysis on genotype-phenotype interplay. Direct links between genotype results and gene expression levels were enriched by detailed analysis of SNP-miRNA-gene interactions at both mature miRNA structure/seed region and target binding site level. The proposed technique was applied to the data on lymphocyte radiation response and increased by almost 100% number of potential functional SNPs.",

keywords = "GWAS, Gene expression, Radiation, Radiosensitivity, Single nucleotide polymorphism, miRNA",

author = "Marzena Dolbniak and Joanna Zyla and Sylwia Kabacik and Grainne Manning and Christophe Badie and Ghazi Alsbeih and Joanna Polanska",

year = "2015",

doi = "10.5220/0005286102430250",

language = "English",

series = "BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015",

publisher = "SciTePress",

pages = "243--250",

editor = "Oscar Pastor and Christine Sinoquet and Ana Fred and Hugo Gamboa and Dirk Elias",

booktitle = "BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015",

note = "6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015 ; Conference date: 12-01-2015 Through 15-01-2015",

}

Dolbniak, M, Zyla, J, Kabacik, S, Manning, G, Badie, C, Alsbeih, G & Polanska, J 2015, Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses? in O Pastor, C Sinoquet, A Fred, H Gamboa & D Elias (eds), BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015. BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015, SciTePress, pp. 243-250, 6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015, Lisbon, Portugal, 12/01/15. https://doi.org/10.5220/0005286102430250

Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses? / Dolbniak, Marzena; Zyla, Joanna; Kabacik, Sylwia et al.

BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015. ed. / Oscar Pastor; Christine Sinoquet; Ana Fred; Hugo Gamboa; Dirk Elias. SciTePress, 2015. p. 243-250 (BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review