Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.
Post-translational modifications (PTMs) are one of the main contributors to the diversity of proteoforms in the proteomic landscape. In particular, protein phosphorylation represents an essential regulatory mechanism that plays a role in many biological processes. Protein kinases, the enzymes catalyzing this reaction, are key participants in metabolic and signaling pathways. Their activation or inactivation dictate downstream events: what substrates are modified and their subsequent impact (e.g., activation state, localization, protein-protein interactions (PPIs)). The biomedical literature continues to be the main source of evidence for experimental information about protein phosphorylation. Automatic methods to bring together phosphorylation events and phosphorylation-dependent PPIs can help to summarize the current knowledge and to expose hidden connections. In this chapter, we demonstrate two text mining tools, RLIMS-P and eFIP, for the retrieval and extraction of kinase-substrate-site data and phosphorylation-dependent PPIs from the literature. These tools offer several advantages over a literature search in PubMed as their results are specific for phosphorylation. RLIMS-P and eFIP results can be sorted, organized, and viewed in multiple ways to answer relevant biological questions, and the protein mentions are linked to UniProt identifiers.
Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE, 19711, USA.|Department of Computer & Information Sciences, University of Delaware, Newark, DE, 19711, USA.
Qinghua
Q
Wang
Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20057, USA.
Karen E
KE
Ross
Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE, 19711, USA.|Department of Computer & Information Sciences, University of Delaware, Newark, DE, 19711, USA.
Hongzhan
H
Huang
Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE, 19711, USA.
Jia
J
Ren
Department of Computer & Information Sciences, University of Delaware, Newark, DE, 19711, USA.
Gang
G
Li
Department of Computer & Information Sciences, University of Delaware, Newark, DE, 19711, USA.
K
K
Vijay-Shanker
Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE, 19711, USA.|Department of Computer & Information Sciences, University of Delaware, Newark, DE, 19711, USA.|Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20057, USA.
Cathy H
CH
Wu
Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE, 19711, USA. arighi@dbi.udel.edu.|Department of Computer & Information Sciences, University of Delaware, Newark, DE, 19711, USA. arighi@dbi.udel.edu.
Cecilia N
CN
Arighi
D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D010750:Phosphoproteins / Q000378:metabolism*; D010766:Phosphorylation; D011485:Protein Binding; D025941:Protein Interaction Mapping; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
D010750:Phosphoproteins; D011506:Proteins
Bioinformatics; Phosphorylation; Post-translational modification; Protein–protein interaction; Text mining