piNET: a versatile web platform for downstream analysis and visualization of proteomics data.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
02 07 2020
02 07 2020
Historique:
accepted:
27
05
2020
revised:
29
04
2020
received:
25
03
2020
pubmed:
30
5
2020
medline:
2
10
2020
entrez:
30
5
2020
Statut:
ppublish
Résumé
Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for the server consists of a set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Several interconnected workflows can be used to generate: (i) interactive graphs and tables providing comprehensive annotation and mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualization for enzyme-substrate networks, including kinases and their phospho-peptide targets; (iii) mapping and visualization of LINCS signature connectivity for chemical inhibitors or genetic knockdown of enzymes upstream of their target PTM sites. piNET has been built using a modular Spring-Boot JAVA platform as a fast, versatile and easy to use tool. The Apache Lucene indexing is used for fast mapping of peptides into UniProt entries for the human, mouse and other commonly used model organism proteomes. PTM-centric network analyses combine PhosphoSitePlus, iPTMnet and SIGNOR databases of validated enzyme-substrate relationships, for kinase networks augmented by DeepPhos predictions and sequence-based mapping of PhosphoSitePlus consensus motifs. Concordant LINCS signatures are mapped using iLINCS. For each workflow, a RESTful API counterpart can be used to generate the results programmatically in the json format. The server is available at http://pinet-server.org, and it is free and open to all users without login requirement.
Identifiants
pubmed: 32469073
pii: 5848491
doi: 10.1093/nar/gkaa436
pmc: PMC7319557
doi:
Substances chimiques
Enzymes
0
Peptides
0
Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
W85-W93Subventions
Organisme : NCATS NIH HHS
ID : UL1 TR001425
Pays : United States
Organisme : NHLBI NIH HHS
ID : U54 HL127624
Pays : United States
Organisme : NIEHS NIH HHS
ID : P30 ES006096
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA236764
Pays : United States
Organisme : NIGMS NIH HHS
ID : U01 GM120953
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH107487
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Nucleic Acids Res. 2016 Jan 4;44(D1):D548-54
pubmed: 26467481
Bioinformatics. 2013 Nov 1;29(21):2808-9
pubmed: 23958731
Nucleic Acids Res. 2011 Jan;39(Database issue):D261-7
pubmed: 21062810
Nucleic Acids Res. 2019 Jan 8;47(D1):D451-D458
pubmed: 30380102
Cell Syst. 2018 Jan 24;6(1):13-24
pubmed: 29199020
Nat Methods. 2014 Jun;11(6):603-4
pubmed: 24874572
Nucleic Acids Res. 2011 Jan;39(Database issue):D253-60
pubmed: 21081558
Proteomics. 2015 Mar;15(5-6):930-49
pubmed: 25158685
Nat Biotechnol. 2015 Jan;33(1):22-4
pubmed: 25574629
Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):449-72
pubmed: 27049628
Mol Cell Proteomics. 2019 Mar;18(3):576-593
pubmed: 30563849
Nucleic Acids Res. 2019 Jan 8;47(D1):D433-D441
pubmed: 30445427
Nucleic Acids Res. 2018 Jan 4;46(D1):D558-D566
pubmed: 29140462
BMC Bioinformatics. 2013 Apr 15;14:128
pubmed: 23586463
Bioinformatics. 2019 Aug 15;35(16):2766-2773
pubmed: 30601936
Proteomics. 2010 May;10(9):1880-5
pubmed: 20198642
Bioinformatics. 2015 Sep 1;31(17):2903-5
pubmed: 25910694
Proteomics. 2015 Sep;15(18):3193-208
pubmed: 26097198
Nucleic Acids Res. 2013 Jan;41(Database issue):D344-7
pubmed: 23161676
Nat Biotechnol. 2008 Dec;26(12):1339-40
pubmed: 19060867
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
Nucleic Acids Res. 2019 Jan 8;47(D1):D529-D541
pubmed: 30476227
Proteomics. 2015 Mar;15(5-6):964-80
pubmed: 25430050
Nat Protoc. 2016 Dec;11(12):2301-2319
pubmed: 27809316
Nucleic Acids Res. 2018 Jan 4;46(D1):D542-D550
pubmed: 29145615
Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7
pubmed: 27141961
Nucleic Acids Res. 2019 Jan 8;47(D1):D298-D308
pubmed: 30418626
Nucleic Acids Res. 2011 Jan;39(Database issue):D777-87
pubmed: 21037261
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W362-5
pubmed: 16845026
Nat Methods. 2016 Sep;13(9):731-40
pubmed: 27348712
Nat Methods. 2013 Mar;10(3):186-7
pubmed: 23443629
Nature. 2016 Sep 14;537(7620):347-55
pubmed: 27629641
Science. 2006 Sep 29;313(5795):1929-35
pubmed: 17008526
Mol Cell Proteomics. 2016 May;15(5):1622-41
pubmed: 26912667