Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces

Bioinformatics
Miguel VázquezTirso Pons

Abstract

The interpretation of cancer-related single-nucleotide variants (SNVs) considering the protein features they affect, such as known functional sites, protein-protein interfaces, or relation with already annotated mutations, might complement the annotation of genetic variants in the analysis of NGS data. Current tools that annotate mutations fall short on several aspects, including the ability to use protein structure information or the interpretation of mutations in protein complexes. We present the Structure-PPi system for the comprehensive analysis of coding SNVs based on 3D protein structures of protein complexes. The 3D repository used, Interactome3D, includes experimental and modeled structures for proteins and protein-protein complexes. Structure-PPi annotates SNVs with features extracted from UniProt, InterPro, APPRIS, dbNSFP and COSMIC databases. We illustrate the usefulness of Structure-PPi with the interpretation of 1 027 122 non-synonymous SNVs from COSMIC and the 1000G Project that provides a collection of ∼172 700 SNVs mapped onto the protein 3D structure of 8726 human proteins (43.2% of the 20 214 SwissProt-curated proteins in UniProtKB release 2014_06) and protein-protein interfaces with potential functional impli...Continue Reading

References

Dec 21, 2004·Nucleic Acids Research·Joke ReumersFrederic Rousseau
May 10, 2005·Bioinformatics·Carles Ferrer-CostaModesto Orozco
Mar 23, 2006·BMC Bioinformatics·Peng YueJohn Moult
Apr 1, 2010·Nature Methods·Ivan A AdzhubeiShamil R Sunyaev
Oct 19, 2010·Nucleic Acids Research·Simon A ForbesP Andrew Futreal
Mar 19, 2011·Cell·Marc VidalAlbert-László Barabási
Nov 19, 2011·Nucleic Acids Research·Sarah HunterSiew-Yit Yong
Nov 20, 2012·Nucleic Acids Research·Jose Manuel RodriguezMichael L Tress
Nov 20, 2012·Nucleic Acids Research·UNKNOWN UniProt Consortium
Feb 13, 2013·Nature Methods·Roberto MoscaPatrick Aloy
Jul 23, 2013·Journal of Molecular Biology·Christopher M Yates, Michael J E Sternberg
Jul 31, 2013·Journal of Molecular Biology·Maximilian HechtBurkhard Rost
Nov 14, 2014·Nucleic Acids Research·Eduard Porta-PardoAdam Godzik
Feb 27, 2015·Nature Methods·Roberto MoscaPatrick Aloy

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Citations

Jul 26, 2015·Bioinformatics·Arnaud Céol, Heiko Müller
Dec 16, 2016·Nature Reviews. Cancer·Andrea Califano, Mariano J Alvarez
Jan 10, 2017·Expert Opinion on Drug Discovery·Sehee Choi, Kang-Yell Choi
May 13, 2017·Briefings in Bioinformatics·Igor B RogozinDavid N Cooper
Jul 18, 2017·Nature Methods·Eduard Porta-PardoAdam Godzik
Jan 30, 2018·Expert Opinion on Drug Discovery·Mireia Rosell, Juan Fernández-Recio
Oct 8, 2015·Human Mutation·Miguel VazquezJose M G Izarzugaza
Jun 4, 2017·International Journal of Cancer. Journal International Du Cancer·Gardenia M Vargas-ParraGabriel Capellá
Jul 17, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Bruna CalsinaMercedes Robledo
Dec 15, 2018·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Emidio CapriottiHannah Carter
Feb 9, 2018·The Journal of Physical Chemistry. B·Zhe WangTingjun Hou

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Software Mentioned

SIFT
PolyPhen
Interactome3D
FATHMM
dbNSFP
MutationTaster
COSMIC
VEST3
PoPMuSiC
Polyphen2

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