IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
07 01 2022
07 01 2022
Historique:
accepted:
03
11
2021
revised:
13
10
2021
received:
15
09
2021
pubmed:
11
11
2021
medline:
24
2
2022
entrez:
10
11
2021
Statut:
ppublish
Résumé
Improved bioassays have significantly increased the rate of identifying new protein-protein interactions (PPIs), and the number of detected human PPIs has greatly exceeded early estimates of human interactome size. These new PPIs provide a more complete view of disease mechanisms but precise understanding of how PPIs affect phenotype remains a challenge. It requires knowledge of PPI context (e.g. tissues, subcellular localizations), and functional roles, especially within pathways and protein complexes. The previous IID release focused on PPI context, providing networks with comprehensive tissue, disease, cellular localization, and druggability annotations. The current update adds developmental stages to the available contexts, and provides a way of assigning context to PPIs that could not be previously annotated due to insufficient data or incompatibility with available context categories (e.g. interactions between membrane and cytoplasmic proteins). This update also annotates PPIs with conservation across species, directionality in pathways, membership in large complexes, interaction stability (i.e. stable or transient), and mutation effects. Enrichment analysis is now available for all annotations, and includes multiple options; for example, context annotations can be analyzed with respect to PPIs or network proteins. In addition to tabular view or download, IID provides online network visualization. This update is available at http://ophid.utoronto.ca/iid.
Identifiants
pubmed: 34755877
pii: 6424757
doi: 10.1093/nar/gkab1034
pmc: PMC8728267
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D640-D647Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
J Clin Bioinforma. 2012 Jan 13;2(1):1
pubmed: 22239822
Cell. 2014 Nov 20;159(5):1212-1226
pubmed: 25416956
BMC Syst Biol. 2012 Jul 30;6:92
pubmed: 22846459
Nucleic Acids Res. 2021 Jan 8;49(D1):D884-D891
pubmed: 33137190
PLoS Comput Biol. 2012;8(9):e1002694
pubmed: 23028291
Genome Biol. 2006;7(11):120
pubmed: 17147767
Cancer Biol Ther. 2009 Feb;8(4):312-8
pubmed: 19202349
Mol Cell Proteomics. 2011 Nov;10(11):M111.010629
pubmed: 21836163
Nucleic Acids Res. 2019 Jan 8;47(D1):D559-D563
pubmed: 30357367
Nature. 2002 May 23;417(6887):399-403
pubmed: 12000970
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51
pubmed: 14681454
Wiley Interdiscip Rev Syst Biol Med. 2020 Nov;12(6):e1489
pubmed: 32307915
Genome Biol. 2010 Jan 12;11(1):R3
pubmed: 20067622
Curr Opin Biotechnol. 2020 Jun;63:177-189
pubmed: 32199228
Genome Biol. 2005;6(1):R2
pubmed: 15642094
Cell. 2012 Aug 31;150(5):1068-81
pubmed: 22939629
Nat Genet. 2015 Jun;47(6):569-76
pubmed: 25915600
Nucleic Acids Res. 2013 Jan;41(Database issue):D1228-33
pubmed: 23180781
Nucleic Acids Res. 2019 Jan 8;47(D1):D433-D441
pubmed: 30445427
PLoS Comput Biol. 2009 Apr;5(4):e1000350
pubmed: 19503817
Database (Oxford). 2019 Jan 1;2019:
pubmed: 30715274
Cell. 2018 Jun 14;173(7):1581-1592
pubmed: 29887378
J Immunol. 2012 Nov 1;189(9):4612-20
pubmed: 23024273
Bioinformatics. 2016 Apr 15;32(8):1262-4
pubmed: 26685306
Nucleic Acids Res. 2015 Jul 1;43(W1):W258-63
pubmed: 25990735
Biochem Pharmacol. 2019 Oct;168:384-391
pubmed: 31381872
Nat Commun. 2019 Jan 2;10(1):10
pubmed: 30602777
Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63
pubmed: 24234451
Genome Biol. 2008;9 Suppl 1:S7
pubmed: 18613951
Nat Biotechnol. 2010 Sep;28(9):935-42
pubmed: 20829833
Nat Commun. 2020 Jul 14;11(1):3518
pubmed: 32665542
Nat Methods. 2015 Jan;12(1):79-84
pubmed: 25402006
Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72
pubmed: 18988627
BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):395
pubmed: 27766938
Nat Commun. 2020 Jan 24;11(1):499
pubmed: 31980649
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Cell. 2015 Jul 16;162(2):425-440
pubmed: 26186194
PLoS Comput Biol. 2012;8(9):e1002690
pubmed: 23028288
Nucleic Acids Res. 2018 Jan 4;46(D1):D601-D607
pubmed: 29165593
Mol Syst Biol. 2009;5:260
pubmed: 19357639
Database (Oxford). 2010 Oct 12;2010:baq023
pubmed: 20940177
Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5
pubmed: 23193258
Nucleic Acids Res. 2017 Jan 4;45(D1):D408-D414
pubmed: 27794551
Sci Rep. 2015 Nov 30;5:17417
pubmed: 26615774
Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503
pubmed: 31691815
Nucleic Acids Res. 2021 Jan 8;49(D1):D325-D334
pubmed: 33290552
Nucleic Acids Res. 2012 Jan;40(Database issue):D857-61
pubmed: 22096227
Genome Res. 2011 Jul;21(7):1109-21
pubmed: 21536720
Nat Commun. 2021 May 31;12(1):3258
pubmed: 34059679
J Pathol. 2016 Oct;240(2):161-72
pubmed: 27357447
Nat Methods. 2009 Jan;6(1):83-90
pubmed: 19060904
Proteomics. 2012 May;12(10):1687-96
pubmed: 22589215
Nat Biotechnol. 2005 Aug;23(8):951-9
pubmed: 16082366
Methods. 2018 Aug 1;145:41-50
pubmed: 29874547
Bioinformatics. 2018 Nov 15;34(22):3873-3881
pubmed: 29868758
Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9
pubmed: 18832364
Sci Immunol. 2019 Jun 7;4(36):
pubmed: 31175175
Nat Commun. 2020 Dec 1;11(1):6144
pubmed: 33262342
Nucleic Acids Res. 2019 Jan 8;47(D1):D581-D589
pubmed: 30407591
Bioinformatics. 2009 Dec 15;25(24):3327-9
pubmed: 19837718
Nature. 2020 Apr;580(7803):402-408
pubmed: 32296183
Nucleic Acids Res. 2021 Jan 8;49(D1):D605-D612
pubmed: 33237311
Int J Gynecol Cancer. 2019 Feb;29(2):346-352
pubmed: 30659026
Eur J Rheumatol. 2017 Dec;4(4):272-277
pubmed: 29308283
Nucleic Acids Res. 2020 Jan 8;48(D1):D845-D855
pubmed: 31680165
Nature. 2012 Oct 25;490(7421):556-60
pubmed: 23023127
Nucleic Acids Res. 2017 Jan 4;45(D1):D427-D431
pubmed: 27899616
Bioinformatics. 2010 Apr 15;26(8):1057-63
pubmed: 20185403
Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489
pubmed: 33237286
Nat Rev Genet. 2017 Sep;18(9):551-562
pubmed: 28607512
Genome Res. 2010 Jun;20(6):804-15
pubmed: 20219939
Nucleic Acids Res. 2019 Jan 8;47(D1):D376-D381
pubmed: 30371822
Nature. 2017 May 25;545(7655):505-509
pubmed: 28514442
Protein Sci. 2021 Jan;30(1):187-200
pubmed: 33070389
Immunity. 2020 Nov 17;53(5):1108-1122.e5
pubmed: 33128875
Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082
pubmed: 29126136
Nat Commun. 2020 May 15;11(1):2440
pubmed: 32415080
Clin Exp Rheumatol. 2004 Jul-Aug;22(4):389-94
pubmed: 15301233