title: PTP-central: a comprehensive resource of protein tyrosine phosphatases in eukaryotic genomes.
abstract: Reversible tyrosine phosphorylation is a fundamental signaling mechanism controlling a diversity of cellular processes. Whereas protein tyrosine kinases have long been implicated in many diseases, aberrant protein tyrosine phosphatase (PTP) activity is also increasingly being associated with a wide spectrum of conditions. PTPs are now regarded as key regulators of biochemical processes instead of simple "off" switches operating in tyrosine kinase signaling pathways. Despite the central importance that PTPs play in the cell's biochemistry, the tyrosine phosphatomes of most species remain uncharted. Here we present a highly sensitive and specific sequence-based method for the automatic classification of PTPs. As proof of principle we re-annotated the human tyrosine phosphatome, and discovered four new PTP genes that had not been reported before. Our method and the predicted tyrosine phosphatomes of 65 eukaryotic genomes are accessible online through the user-friendly PTP-central resource (http://www.PTP-central.org/), where users can also submit their own sequences for prediction. PTP-central is a comprehensive and continually developing resource that currently integrates the predicted tyrosine phosphatomes with structural data and genetic association disease studies, as well as homology relationships. PTP-central thus fills an important void for the systematic study of PTPs, both in model organisms and from an evolutionary perspective.
authors.affiliation: Goodman Cancer Research Center, McGill University, 1160 Pine Avenue, Montreal H3A 1A3, QC, Canada; Department of Biochemistry, McGill University, Montreal, QC, Canada.
authors.forename: Teri
authors.initials: T
authors.lastname: Hatzihristidis
authors.affiliation: Bioinformatics and Genomics Laboratory, World Premier International (WPI), Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan.
authors.forename: Shaq
authors.initials: S
authors.lastname: Liu
authors.affiliation: Centre for Genomic Regulation (CRG), UPF, Dr. Aiguader, 88, 08003 Barcelona, Spain.
authors.forename: Leszek
authors.initials: L
authors.lastname: Pryszcz
authors.affiliation: Bioinformatics and Genomics Laboratory, World Premier International (WPI), Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Hutchins
authors.affiliation: Centre for Genomic Regulation (CRG), UPF, Dr. Aiguader, 88, 08003 Barcelona, Spain.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: Goodman Cancer Research Center, McGill University, 1160 Pine Avenue, Montreal H3A 1A3, QC, Canada; Department of Biochemistry, McGill University, Montreal, QC, Canada. Electronic address: michel.tremblay@mcgill.ca.
authors.forename: Michel L
authors.initials: ML
authors.lastname: Tremblay
authors.affiliation: Bioinformatics and Genomics Laboratory, World Premier International (WPI), Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan. Electronic address: diego@ifrec.osaka-u.ac.jp.
authors.forename: Diego
authors.initials: D
authors.lastname: Miranda-Saavedra
mesh_terms: D000818:Animals; D019992:Databases as Topic; D056726:Genetic Association Studies; D016678:Genome / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D017027:Protein Tyrosine Phosphatases / Q000737:chemistry / Q000235:genetics*
chemical_list: D017027:Protein Tyrosine Phosphatases
keywords: Database; HMM; Sequence analysis; Signal transduction; Tyrosine phosphatase; Tyrosine phosphorylation