PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction

Scientific Reports
Ying XuJames C Whisstock

Abstract

Phosphorylation is the most important type of protein post-translational modification. Accordingly, reliable identification of kinase-mediated phosphorylation has important implications for functional annotation of phosphorylated substrates and characterization of cellular signalling pathways. The local sequence context surrounding potential phosphorylation sites is considered to harbour the most relevant information for phosphorylation site prediction models. However, currently there is a lack of condensed vector representation for this important contextual information, despite the presence of varying residue-level features that can be constructed from sequence homology profiles, structural information, and physicochemical properties. To address this issue, we present PhosContext2vec which is a distributed representation of residue-level sequence contexts for potential phosphorylation sites and demonstrate its application in both general and kinase-specific phosphorylation site predictions. Benchmarking experiments indicate that PhosContext2vec could achieve promising predictive performance compared with several other existing methods for phosphorylation site prediction. We envisage that PhosContext2vec, as a new sequence cont...Continue Reading

References

Aug 20, 1988·Journal of Molecular Biology·N Qian, T J Sejnowski
Mar 21, 1986·Journal of Theoretical Biology·W R Taylor
Dec 25, 1983·Journal of Molecular Biology·R M Sweet, D Eisenberg
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 23, 1997·Neural Computation·S Hochreiter, J Schmidhuber
Dec 10, 1998·Nucleic Acids Research·A KreegipuuS Brunak
Dec 22, 1999·Journal of Molecular Biology·N BlomS Brunak
Sep 17, 2002·Briefings in Bioinformatics·Christian J A SigristPhilipp Bucher
Mar 29, 2003·Neural Networks : the Official Journal of the International Neural Network Society·Y Liu, X Yao
Feb 13, 2004·Nucleic Acids Research·Lilia M IakouchevaA Keith Dunker
Mar 24, 2004·Journal of Molecular Biology·I MihalekO Lichtarge
Nov 24, 2004·Biochemical and Biophysical Research Communications·Feng-Feng ZhouXuebiao Yao
Jun 28, 2005·Nucleic Acids Research·Hsien-Da HuangJorng-Tzong Horng
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Mar 9, 2007·Nature Biotechnology·Ramars AmanchyAkhilesh Pandey
Jun 23, 2007·Nature Reviews. Molecular Cell Biology·Jeffrey A Ubersax, James E Ferrell
May 9, 2008·Molecular & Cellular Proteomics : MCP·Yu XueXuebiao Yao
Nov 8, 2008·Nucleic Acids Research·T S Keshava PrasadAkhilesh Pandey
Dec 9, 2008·Nature Biotechnology·Bernd BodenmillerRuedi Aebersold
Nov 3, 2009·Nucleic Acids Research·Pawel DurekWaltraud X Schulze
Feb 5, 2010·Bioinformatics·Jiangning SongJames C Whisstock
Jul 29, 2010·BMC Bioinformatics·Fredrik Johansson, Hiroyuki Toh
Aug 13, 2010·Molecular & Cellular Proteomics : MCP·Jianjiong GaoDong Xu
Nov 3, 2010·Nucleic Acids Research·Tzong-Yi LeeHsien-Da Huang
Nov 11, 2010·Protein Engineering, Design & Selection : PEDS·Yu XueJian Ren
Nov 11, 2010·Nucleic Acids Research·Holger DinkelFrancesca Diella
Nov 15, 2011·Cell·Samuel M PearlmanJames E Ferrell
Jun 12, 2013·Nucleic Acids Research·Daniel W A BuchanDavid T Jones
Oct 24, 2013·Bioinformatics·Mingjun WangJiangning Song
Nov 15, 2013·Nature Communications·Elisa CiliaWim F Vranken
Oct 29, 2014·Nucleic Acids Research·UNKNOWN UniProt Consortium
Nov 14, 2014·Bioinformatics·David T Jones, Domenico Cozzetto
Jul 2, 2016·Journal of Proteome Research·Brett TrostScott Napper
Jan 4, 2017·Briefings in Bioinformatics·Yuedong YangYaoqi Zhou

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Citations

Dec 24, 2018·Briefings in Functional Genomics·Wenying HeQuan Zou
Dec 19, 2019·BMC Bioinformatics·Michael HeinzingerBurkhard Rost
Dec 15, 2020·Briefings in Functional Genomics·Chunyan AoQuan Zou
Apr 4, 2021·International Journal of Molecular Sciences·Noam AuslanderEugene V Koonin
Oct 26, 2021·Journal of Bioinformatics and Computational Biology·Hrushikesh BhosaleValadi K Jayaraman

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Methods Mentioned

BETA
feature extraction

Software Mentioned

BLAST
PhosContext2vec
Context2vec add
ProtVet
GPS
Musite
KinasePhos
PhosphoPick
Context2vec inference
word2vec

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