Linear Motif Atlas for Phosphorylation-Dependent Signaling

Martin Lee Miller,^1,2* Lars Juhl Jensen,^2,3* Francesca Diella,³ Claus Jørgensen,⁴ Michele Tinti,⁵ Lei Li,⁶ Marilyn Hsiung,⁴ Sirlester A. Parker,⁷ Jennifer Bordeaux,⁷ Thomas Sicheritz-Ponten,¹ Marina Olhovsky,⁴ Adrian Pasculescu,⁴ Jes Alexander,⁸ Stefan Knapp,⁹ Nikolaj Blom,¹ Peer Bork,^2,10 Shawn Li,⁶ Gianni Cesareni,⁵ Tony Pawson,⁴ Benjamin E. Turk,⁷ Michael B. Yaffe,^8† Søren Brunak,^1,2† Rune Linding^4,8,11†

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.

⁵Uni versity 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.

*These authors contributed equally to this work

Supplementary Figures, Tables, and Poster PDF

• Figure S1: Overview of the NetPhorest pipeline.
• Figure S2: Phosphorylation data mapped onto domain trees.
• Figure S3: Coverage of classifiers for targets of kinases, SH2 domains, and PTB domains.
• Figure S4: Score calibration.
• Figure S5: Correlation between domain similarity and substrate specificity.
• Figure S6: Kinase matrices from Positional Scanning Peptide Libraries (PSPL).
• Figure S7: Sequence logos for kinases and pS/pT-binding domains.
• Figure S8: Receiver output characteristic (ROC) curves for the NetPhorest classifiers.
• Table S1: The selected set of NetPhorest classifiers.
• Table S2: Benchmark of the NetPhorest method.
• Poster: A Sequence-Specificity Atlas of the Kinase World

Technical Details

Format: Adobe Acrobat PDF

Size: 17.4 MB

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Update 28 October 2008

The Supplementary Materials are now available as separate PDFs to facilitate download of the files. In addition, a sponsored version of the poster was distributed in the September 2008 print compilation of Science Signaling and in the 17 October 2008 issue of Science. The sponsored version of the poster is now available as a PDF.

• Supplementary Figures and Tables Only PDF (2.11 MB). [Download PDF]
• Original Supplementary Poster PDF (14.2 MB) [Download PDF]
• Sponsored Poster PDF (1.6 MB) [Download PDF]

†Corresponding authors. E-mail, brunak{at}cbs.dtu.dk (S.B.), myaffe{at}mit.edu (M.B.Y.), and rune.linding{at}gmail.com (R.L.)

Citation: M. L. Miller, L. J. Jensen, F. Diella, C. Jørgensen, M. Tinti, L. Li, M. Hsiung, S. A. Parker, J. Bordeaux, T. Sicheritz-Ponten, M. Olhovsky, A. Pasculescu, J. Alexander, S. Knapp, N. Blom, P. Bork, S. Li, G. Cesareni, T. Pawson, B. E. Turk, M. B. Yaffe, S. Brunak, R. Linding, Linear Motif Atlas for Phosphorylation-Dependent Signaling. Sci. Signal. 1, ra2 (2008).

© 2008 American Association for the Advancement of Science