Systematic discovery of in vivo phosphorylation networks

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Systematic discovery of in vivo phosphorylation networks. / Linding, Rune; Jensen, Lars Juhl; Ostheimer, Gerard J; van Vugt, Marcel A T M; Jørgensen, Claus; Miron, Ioana M; Diella, Francesca; Colwill, Karen; Taylor, Lorne; Elder, Kelly; Metalnikov, Pavel; Nguyen, Vivian; Pasculescu, Adrian; Jin, Jing; Park, Jin Gyoon; Samson, Leona D; Woodgett, James R; Russell, Robert B; Bork, Peer; Yaffe, Michael B; Pawson, Tony.

In: Cell, Vol. 129, No. 7, 2007, p. 1415-26.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Linding, R, Jensen, LJ, Ostheimer, GJ, van Vugt, MATM, Jørgensen, C, Miron, IM, Diella, F, Colwill, K, Taylor, L, Elder, K, Metalnikov, P, Nguyen, V, Pasculescu, A, Jin, J, Park, JG, Samson, LD, Woodgett, JR, Russell, RB, Bork, P, Yaffe, MB & Pawson, T 2007, 'Systematic discovery of in vivo phosphorylation networks', Cell, vol. 129, no. 7, pp. 1415-26. https://doi.org/10.1016/j.cell.2007.05.052

APA

Linding, R., Jensen, L. J., Ostheimer, G. J., van Vugt, M. A. T. M., Jørgensen, C., Miron, I. M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J. G., Samson, L. D., Woodgett, J. R., Russell, R. B., Bork, P., ... Pawson, T. (2007). Systematic discovery of in vivo phosphorylation networks. Cell, 129(7), 1415-26. https://doi.org/10.1016/j.cell.2007.05.052

Vancouver

Linding R, Jensen LJ, Ostheimer GJ, van Vugt MATM, Jørgensen C, Miron IM et al. Systematic discovery of in vivo phosphorylation networks. Cell. 2007;129(7):1415-26. https://doi.org/10.1016/j.cell.2007.05.052

Author

Linding, Rune ; Jensen, Lars Juhl ; Ostheimer, Gerard J ; van Vugt, Marcel A T M ; Jørgensen, Claus ; Miron, Ioana M ; Diella, Francesca ; Colwill, Karen ; Taylor, Lorne ; Elder, Kelly ; Metalnikov, Pavel ; Nguyen, Vivian ; Pasculescu, Adrian ; Jin, Jing ; Park, Jin Gyoon ; Samson, Leona D ; Woodgett, James R ; Russell, Robert B ; Bork, Peer ; Yaffe, Michael B ; Pawson, Tony. / Systematic discovery of in vivo phosphorylation networks. In: Cell. 2007 ; Vol. 129, No. 7. pp. 1415-26.

Bibtex

@article{c48fc99d21304fe8adc08e5a4dfdf03f,
title = "Systematic discovery of in vivo phosphorylation networks",
abstract = "Protein kinases control cellular decision processes by phosphorylating specific substrates. Thousands of in vivo phosphorylation sites have been identified, mostly by proteome-wide mapping. However, systematically matching these sites to specific kinases is presently infeasible, due to limited specificity of consensus motifs, and the influence of contextual factors, such as protein scaffolds, localization, and expression, on cellular substrate specificity. We have developed an approach (NetworKIN) that augments motif-based predictions with the network context of kinases and phosphoproteins. The latter provides 60%-80% of the computational capability to assign in vivo substrate specificity. NetworKIN pinpoints kinases responsible for specific phosphorylations and yields a 2.5-fold improvement in the accuracy with which phosphorylation networks can be constructed. Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate.",
author = "Rune Linding and Jensen, {Lars Juhl} and Ostheimer, {Gerard J} and {van Vugt}, {Marcel A T M} and Claus J{\o}rgensen and Miron, {Ioana M} and Francesca Diella and Karen Colwill and Lorne Taylor and Kelly Elder and Pavel Metalnikov and Vivian Nguyen and Adrian Pasculescu and Jing Jin and Park, {Jin Gyoon} and Samson, {Leona D} and Woodgett, {James R} and Russell, {Robert B} and Peer Bork and Yaffe, {Michael B} and Tony Pawson",
year = "2007",
doi = "10.1016/j.cell.2007.05.052",
language = "English",
volume = "129",
pages = "1415--26",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "7",

}

RIS

TY - JOUR

T1 - Systematic discovery of in vivo phosphorylation networks

AU - Linding, Rune

AU - Jensen, Lars Juhl

AU - Ostheimer, Gerard J

AU - van Vugt, Marcel A T M

AU - Jørgensen, Claus

AU - Miron, Ioana M

AU - Diella, Francesca

AU - Colwill, Karen

AU - Taylor, Lorne

AU - Elder, Kelly

AU - Metalnikov, Pavel

AU - Nguyen, Vivian

AU - Pasculescu, Adrian

AU - Jin, Jing

AU - Park, Jin Gyoon

AU - Samson, Leona D

AU - Woodgett, James R

AU - Russell, Robert B

AU - Bork, Peer

AU - Yaffe, Michael B

AU - Pawson, Tony

PY - 2007

Y1 - 2007

N2 - Protein kinases control cellular decision processes by phosphorylating specific substrates. Thousands of in vivo phosphorylation sites have been identified, mostly by proteome-wide mapping. However, systematically matching these sites to specific kinases is presently infeasible, due to limited specificity of consensus motifs, and the influence of contextual factors, such as protein scaffolds, localization, and expression, on cellular substrate specificity. We have developed an approach (NetworKIN) that augments motif-based predictions with the network context of kinases and phosphoproteins. The latter provides 60%-80% of the computational capability to assign in vivo substrate specificity. NetworKIN pinpoints kinases responsible for specific phosphorylations and yields a 2.5-fold improvement in the accuracy with which phosphorylation networks can be constructed. Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate.

AB - Protein kinases control cellular decision processes by phosphorylating specific substrates. Thousands of in vivo phosphorylation sites have been identified, mostly by proteome-wide mapping. However, systematically matching these sites to specific kinases is presently infeasible, due to limited specificity of consensus motifs, and the influence of contextual factors, such as protein scaffolds, localization, and expression, on cellular substrate specificity. We have developed an approach (NetworKIN) that augments motif-based predictions with the network context of kinases and phosphoproteins. The latter provides 60%-80% of the computational capability to assign in vivo substrate specificity. NetworKIN pinpoints kinases responsible for specific phosphorylations and yields a 2.5-fold improvement in the accuracy with which phosphorylation networks can be constructed. Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate.

U2 - 10.1016/j.cell.2007.05.052

DO - 10.1016/j.cell.2007.05.052

M3 - Journal article

C2 - 17570479

VL - 129

SP - 1415

EP - 1426

JO - Cell

JF - Cell

SN - 0092-8674

IS - 7

ER -

ID: 40740342