loading
  • Login
  • Sign-Up

Research.Publish.Connect.

Paper

Authors: Ilya E. Vorontsov 1 ; Ivan V. Kulakovskiy 2 ; Grigory Khimulya 1 ; Daria D. Nikolaeva 3 and Vsevolod J. Makeev 4

Affiliations: 1 Vavilov Institute of General Genetics, Russian Federation ; 2 Vavilov Institute of General Genetics and Engelhardt Institute of Molecular Biology, Russian Federation ; 3 Lomonosov Moscow State University, Russian Federation ; 4 Vavilov Institute of General Genetics, Engelhardt Institute of Molecular Biology and Moscow Institute of Physics and Technology, Russian Federation

ISBN: 978-989-758-070-3

Keyword(s): Single Nucleotide Polymorphism, SNP, Single Nucleotide Variant, SNV, P-value, Transcription Factor Binding Site, TFBS, Position Weight Matrix, PWM, PSSM, Transcriptional Regulation.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Sequence Analysis ; Web Services in Bioinformatics

Abstract: Single nucleotide polymorphisms (SNPs) and variants (SNVs) are often found in regulatory regions of human genome. Nucleotide substitutions in promoter and enhancer regions may affect transcription factor (TF) binding and alter gene expression regulation. Nowadays binding patterns are known for hundreds of human TFs. Thus one can assess possible functional effects of allele variations or mutations in TF binding sites using sequence analysis. We present PERFECTOS-APE, the software to PrEdict Regulatory Functional Effect of SNPs by Approximate P-value Estimation. Using a predefined collection of position weight matrices (PWMs) representing TF binding patterns, PERFECTOS-APE identifies transcription factors whose binding sites can be significantly affected by given nucleotide substitutions. PERFECTOS-APE supports both classic PWMs under the position independency assumption, and dinucleotide PWMs accounting for the dinucleotide composition and correlations between nucleotides in adjacent p ositions within binding sites. PERFECTOS-APE uses dynamic programming to calculate PWM score distribution and convert the scores to P-values with an optional binary search mode using a precomputed P-value list to speed-up the computations. Software is written in Java and is freely available as standalone program and online tool: http://opera.autosome.ru/perfectosape/. We have tested our algorithm on several disease associated SNVs as well as on a set of cancer somatic mutations occurring in intronic regions of the human genome. (More)

PDF ImageFull Text

Download
Sign In Guest: Register as new SCITEPRESS user or Join INSTICC now for free.

Sign In SCITEPRESS user: please login.

Sign In INSTICC Members: please login. If not a member yet, Join INSTICC now for free.

PDF ImageMy Papers

You are not signed in, therefore limits apply to your IP address 54.161.106.81. INSTICC members have higher download limits (free membership now)

In the current month:
Recent papers: 1 available of 1 total
2+ years older papers: 2 available of 2 total

Paper citation in several formats:
E. Vorontsov I., V. Kulakovskiy I., Khimulya G., D. Nikolaeva D. and J. Makeev V. (2015). PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3, pages 102-108. DOI: 10.5220/0005189301020108

@conference{bioinformatics15,
author={Ilya E. Vorontsov and Ivan V. Kulakovskiy and Grigory Khimulya and Daria D. Nikolaeva and Vsevolod J. Makeev},
title={PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)},
year={2015},
pages={102-108},
publisher={ScitePress},
organization={INSTICC},
doi={10.5220/0005189301020108},
isbn={978-989-758-070-3},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)
TI - PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation
SN - 978-989-758-070-3
AU - E. Vorontsov I.
AU - V. Kulakovskiy I.
AU - Khimulya G.
AU - D. Nikolaeva D.
AU - J. Makeev V.
PY - 2015
SP - 102
EP - 108
DO - 10.5220/0005189301020108

Sorted by: Show papers

Note: The preferred Subjects/Areas/Topics, listed below for each paper, are those that match the selected paper topics and their ontology superclasses.
More...

Login or register to post comments.

Comments on this Paper: Be the first to review this paper.

Show authors

Note: The preferred Subjects/Areas/Topics, listed below for each author, are those that more frequently used in the author's papers.
More...