A systematic approach to orient the human protein-protein interaction network.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
09 07 2019
09 07 2019
Historique:
received:
10
02
2018
accepted:
06
06
2019
entrez:
11
7
2019
pubmed:
11
7
2019
medline:
28
10
2019
Statut:
epublish
Résumé
The protein-protein interaction (PPI) network of an organism serves as a skeleton for its signaling circuitry, which mediates cellular response to environmental and genetic cues. Understanding this circuitry could improve the prediction of gene function and cellular behavior in response to diverse signals. To realize this potential, one has to comprehensively map PPIs and their directions of signal flow. While the quality and the volume of identified human PPIs improved dramatically over the last decade, the directions of these interactions are still mostly unknown, thus precluding subsequent prediction and modeling efforts. Here we present a systematic approach to orient the human PPI network using drug response and cancer genomic data. We provide a diffusion-based method for the orientation task that significantly outperforms existing methods. The oriented network leads to improved prioritization of cancer driver genes and drug targets compared to the state-of-the-art unoriented network.
Identifiants
pubmed: 31289271
doi: 10.1038/s41467-019-10887-6
pii: 10.1038/s41467-019-10887-6
pmc: PMC6617457
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3015Références
Nucleic Acids Res. 2015 Jul 1;43(W1):W571-5
pubmed: 25883154
Nat Genet. 2015 Feb;47(2):106-14
pubmed: 25501392
J Comput Biol. 2013 Mar;20(3):249-57
pubmed: 23286509
Bioinformatics. 2010 Oct 1;26(19):2438-44
pubmed: 20709693
Bioinformatics. 2013 Nov 1;29(21):2757-64
pubmed: 23986566
PLoS One. 2014 Mar 13;9(3):e90904
pubmed: 24625764
N Engl J Med. 2013 May 30;368(22):2059-74
pubmed: 23634996
Nature. 1989 Jul 20;340(6230):245-6
pubmed: 2547163
Nat Commun. 2016 Jul 15;7:12096
pubmed: 27417679
Trends Pharmacol Sci. 2005 Apr;26(4):178-82
pubmed: 15808341
Sci Signal. 2011 Oct 25;4(196):pl1
pubmed: 22028466
Nat Rev Genet. 2009 Sep;10(9):617-27
pubmed: 19687803
Database (Oxford). 2011 Nov 30;2011:bar055
pubmed: 22134927
Methods. 2015 Mar;74:83-9
pubmed: 25484339
Nucleic Acids Res. 2011 Mar;39(4):e22
pubmed: 21109539
Genome Biol. 2010 Jan 12;11(1):R3
pubmed: 20067622
Nucleic Acids Res. 2010 Jan;38(Database issue):D497-501
pubmed: 19884131
Diabetes Technol Ther. 2004 Feb;6(1):39-47
pubmed: 15000768
Cell Mol Biol (Noisy-le-grand). 2004 Nov;50(7):805-7
pubmed: 15672464
Nat Biotechnol. 2004 Oct;22(10):1253-9
pubmed: 15470465
Nat Rev Cancer. 2007 Jan;7(1):54-60
pubmed: 17186018
Nature. 2011 Jun 29;474(7353):609-15
pubmed: 21720365
Nat Genet. 2009 Mar;41(3):316-23
pubmed: 19234470
Cancer Res. 2017 Feb 15;77(4):827-838
pubmed: 27965317
Mol Syst Biol. 2009;5:331
pubmed: 19953085
Sci Signal. 2011 Sep 6;4(189):rs8
pubmed: 21900206
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
pubmed: 16381927
Bioinformatics. 2007 Jul 1;23(13):i359-66
pubmed: 17646318
Cell. 2005 Sep 23;122(6):957-68
pubmed: 16169070
Nature. 2012 Oct 4;490(7418):61-70
pubmed: 23000897
Science. 1999 Jan 15;283(5400):381-7
pubmed: 9888852
EMBO Rep. 2013 Nov;14(11):948
pubmed: 24126764
Ann N Y Acad Sci. 2004 May;1020:132-53
pubmed: 15208190
Proteomics. 2004 Jun;4(6):1551-61
pubmed: 15174125
Mol Syst Biol. 2009;5:248
pubmed: 19293828
Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50
pubmed: 20952405
Bioinformatics. 2010 Feb 15;26(4):587-8
pubmed: 20031966
PLoS Comput Biol. 2010 Sep 09;6(9):
pubmed: 20838579
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
PLoS Comput Biol. 2009 Aug;5(8):e1000438
pubmed: 19662154
J Comput Biol. 2011 Nov;18(11):1437-48
pubmed: 21999286
NPJ Syst Biol Appl. 2016 Mar 03;2:16002
pubmed: 28725467
Nature. 2012 Jul 18;487(7407):330-7
pubmed: 22810696
Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12
pubmed: 25348405
J Comput Biol. 2004;11(2-3):243-62
pubmed: 15285891
Bioinformatics. 2014 Jun 15;30(12):i219-27
pubmed: 24931987
Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6
pubmed: 18048412
Nat Rev Genet. 2017 Sep;18(9):551-562
pubmed: 28607512
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
BioData Min. 2011 Jun 24;4:19
pubmed: 21699738
Bioinformatics. 2014 May 15;30(10):1449-55
pubmed: 24470573
Pac Symp Biocomput. 2016;21:156-67
pubmed: 26776182
Cell Syst. 2016 Dec 21;3(6):585-593.e3
pubmed: 28009266