iPTMnet: Integrative Bioinformatics for Studying PTM Networks.
Protein post-translational modification (PTM) is an essential cellular regulatory mechanism, and disruptions in PTM have been implicated in disease. PTMs are an active area of study in many fields, leading to a wealth of PTM information in the scientific literature. There is a need for user-friendly bioinformatics resources that capture PTM information from the literature and support analyses of PTMs and their functional consequences. This chapter describes the use of iPTMnet ( http://proteininformationresource.org/iPTMnet/ ), a resource that integrates PTM information from text mining, curated databases, and ontologies and provides visualization tools for exploring PTM networks, PTM crosstalk, and PTM conservation across species. We present several PTM-related queries and demonstrate how they can be addressed using iPTMnet.
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC, 20057, USA. ker25@georgetown.edu.
Karen E
KE
Ross
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.
Hongzhan
H
Huang
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.
Jia
J
Ren
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.|Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA.
Cecilia N
CN
Arighi
Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA.
Gang
G
Li
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.
Catalina O
CO
Tudor
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.
Mengxi
M
Lv
Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19711, USA.
Jung-Youn
JY
Lee
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.
Sheng-Chih
SC
Chen
Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA.
K
K
Vijay-Shanker
Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC, 20057, USA.|Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.|Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA.
Cathy H
CH
Wu
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D051379:Mice; D010770:Phosphotransferases; D010940:Plant Proteins; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods; D060066:Protein Interaction Maps; D011499:Protein Processing, Post-Translational; D051381:Rats; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
D010940:Plant Proteins; D010770:Phosphotransferases
Acetylation; Database; PTM crosstalk; Phosphorylation; Post-translational modification; Protein ontology; Protein-protein interaction; Text mining