title: Linear motif atlas for phosphorylation-dependent signaling.
abstract: Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14-3-3]. The atlas reveals new aspects of signaling systems, including the observation that tyrosine kinases mutated in cancer have lower specificity than their non-oncogenic relatives. The resource is maintained by an automated pipeline, which uses phylogenetic trees to structure the currently available in vivo and in vitro data to derive probabilistic sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info).
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark.
authors.forename: Martin Lee
authors.initials: ML
authors.lastname: Miller
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.forename: Francesca
authors.initials: F
authors.lastname: Diella
authors.forename: Claus
authors.initials: C
authors.lastname: Jørgensen
authors.forename: Michele
authors.initials: M
authors.lastname: Tinti
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.forename: Marilyn
authors.initials: M
authors.lastname: Hsiung
authors.forename: Sirlester A
authors.initials: SA
authors.lastname: Parker
authors.forename: Jennifer
authors.initials: J
authors.lastname: Bordeaux
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Ponten
authors.forename: Marina
authors.initials: M
authors.lastname: Olhovsky
authors.forename: Adrian
authors.initials: A
authors.lastname: Pasculescu
authors.forename: Jes
authors.initials: J
authors.lastname: Alexander
authors.forename: Stefan
authors.initials: S
authors.lastname: Knapp
authors.forename: Nikolaj
authors.initials: N
authors.lastname: Blom
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Shawn
authors.initials: S
authors.lastname: Li
authors.forename: Gianni
authors.initials: G
authors.lastname: Cesareni
authors.forename: Tony
authors.initials: T
authors.lastname: Pawson
authors.forename: Benjamin E
authors.initials: BE
authors.lastname: Turk
authors.forename: Michael B
authors.initials: MB
authors.lastname: Yaffe
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Rune
authors.initials: R
authors.lastname: Linding