Linear Motif Atlas for Phosphorylation-Dependent Signaling

Martin Lee Miller; Lars Juhl Jensen; Francesca Diella; Claus Jørgensen; Michele Tinti; Lei Li; Marilyn Hsiung; Sirlester A. Parker; Jennifer Bordeaux; Thomas Sicheritz-Ponten; Marina Olhovsky; Adrian Pasculescu; Jes Alexander; Stefan Knapp; Nikolaj Blom; Peer Bork; Shawn Li; Gianni Cesareni; Tony Pawson; Benjamin E. Turk; Michael B. Yaffe; Søren Brunak; Rune Linding

doi:10.1126/scisignal.1159433

Research ArticleCOMPUTATIONAL BIOLOGY

Linear Motif Atlas for Phosphorylation-Dependent Signaling

Martin Lee Miller¹,²,*,
Lars Juhl Jensen²,³,*,
Francesca Diella³,
Claus Jørgensen⁴,
Michele Tinti⁵,
Lei Li⁶,
Marilyn Hsiung⁴,
Sirlester A. Parker⁷,
Jennifer Bordeaux⁷,
Thomas Sicheritz-Ponten¹,
Marina Olhovsky⁴,
Adrian Pasculescu⁴,
Jes Alexander⁸,
Stefan Knapp⁹,
Nikolaj Blom¹,
Peer Bork²,¹⁰,
Shawn Li⁶,
Gianni Cesareni⁵,
Tony Pawson⁴,
Benjamin E. Turk⁷,
Michael B. Yaffe⁸,^†,
Søren Brunak¹,²,^†, and
Rune Linding⁴,⁸,¹¹,^†

¹Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark.
²The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.
³European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
⁴Samuel Lunenfeld Research Institute, Mount Sinai Hospital, M5G 1X5 Toronto, Ontario, Canada.
⁵University of Rome, Tor Vergata, 00133 Rome, Italy.
⁶University of Western Ontario, N6A 5C1 London, Ontario, Canada.
⁷Department of Pharmacology, Yale University School of Medicine, New Haven, 06520 CT, USA.
⁸Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, 021329 MA, USA.
⁹Structural Genomics Consortium, University of Oxford, OX3 7DQ Oxford, UK.
¹⁰Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany.
¹¹Cellular & Molecular Logic Team, The Institute of Cancer Research, SW3 6JB London, UK.

↵†To whom correspondence should be addressed. E-mail: brunak{at}cbs.dtu.dk (S.B.), myaffe{at}mit.edu (M.B.Y.), and rune.linding{at}gmail.com (R.L.)

↵* These authors contributed equally to this work.

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Science Signaling 02 Sep 2008:
Vol. 1, Issue 35, pp. ra2
DOI: 10.1126/scisignal.1159433

Martin Lee Miller

Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark.The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.

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Lars Juhl Jensen

The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

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Francesca Diella

European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

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Claus Jørgensen

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, M5G 1X5 Toronto, Ontario, Canada.

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Michele Tinti

University of Rome, Tor Vergata, 00133 Rome, Italy.

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Lei Li

University of Western Ontario, N6A 5C1 London, Ontario, Canada.

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Marilyn Hsiung

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, M5G 1X5 Toronto, Ontario, Canada.

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Sirlester A. Parker

Department of Pharmacology, Yale University School of Medicine, New Haven, 06520 CT, USA.

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Jennifer Bordeaux

Department of Pharmacology, Yale University School of Medicine, New Haven, 06520 CT, USA.

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Thomas Sicheritz-Ponten

Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark.

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Marina Olhovsky

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, M5G 1X5 Toronto, Ontario, Canada.

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Adrian Pasculescu

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, M5G 1X5 Toronto, Ontario, Canada.

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Jes Alexander

Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, 021329 MA, USA.

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Stefan Knapp

Structural Genomics Consortium, University of Oxford, OX3 7DQ Oxford, UK.

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Nikolaj Blom

Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark.

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Peer Bork

The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany.

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Shawn Li

University of Western Ontario, N6A 5C1 London, Ontario, Canada.

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Gianni Cesareni

University of Rome, Tor Vergata, 00133 Rome, Italy.

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Tony Pawson

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, M5G 1X5 Toronto, Ontario, Canada.

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Benjamin E. Turk

Department of Pharmacology, Yale University School of Medicine, New Haven, 06520 CT, USA.

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Michael B. Yaffe

Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, 021329 MA, USA.

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For correspondence: brunak@cbs.dtu.dk myaffe@mit.edu rune.linding@gmail.com

Søren Brunak

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For correspondence: brunak@cbs.dtu.dk myaffe@mit.edu rune.linding@gmail.com

Rune Linding

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, M5G 1X5 Toronto, Ontario, Canada.Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, 021329 MA, USA.Cellular & Molecular Logic Team, The Institute of Cancer Research, SW3 6JB London, UK.

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For correspondence: brunak@cbs.dtu.dk myaffe@mit.edu rune.linding@gmail.com

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Created with both in vitro and in vivo data, NetPhorest is an atlas of consensus sequence motifs for 179 kinases and 104 phosphorylation-dependent binding domains and reveals new insight into phosphorylation-dependent signaling.

Linear Motif Atlas for Phosphorylation-Dependent Signaling

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