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G. Manning,1*D. B. Whyte,1R. Martinez,1T. Hunter,2S. Sudarsanam13
We have catalogued the protein kinase complement of the
human genome (the "kinome") using public and proprietary genomic,complementary DNA, and expressed sequence tag (EST) sequences.This
provides a starting point for comprehensive analysis of proteinphosphorylation in normal and disease states, as well as a
detailedview of the current state of human genome analysis through a
focuson one large gene family. We identify 518 putative protein kinasegenes, of which 71 have not previously been reported or describedas
kinases, and we extend or correct the protein sequences of56 more
kinases. New genes include members of well-studied familiesas well as
previously unidentified families, some of which areconserved in model
organisms. Classification and comparison withmodel organism kinomes
identified orthologous groups and highlightedexpansions specific to
human and other lineages. We also identified106 protein kinase
pseudogenes. Chromosomal mapping revealed severalsmall clusters of
kinase genes and revealed that 244 kinases mapto disease loci or
cancer amplicons.
1 SUGEN Inc., 230 East Grand Avenue, South San
Francisco, CA 94080, USA.
2 Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
3 Genomics
and Biotechnology, Pharmacia Corporation, 230 East Grand Avenue, South
San Francisco, CA 94080, USA.
*
To whom correspondence should be addressed. E-mail:
gerard-manning{at}sugen.com
Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach.
L. Li, C. Wu, H. Huang, K. Zhang, J. Gan, and S. S.-C. Li (2008)
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Defining the Specificity Space of the Human Src Homology 2 Domain.
H. Huang, L. Li, C. Wu, D. Schibli, K. Colwill, S. Ma, C. Li, P. Roy, K. Ho, Z. Songyang, et al. (2008)
Mol. Cell. Proteomics
7, 768-784
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Ca2+/Calmodulin-Dependent Protein Kinase II{delta} and Protein Kinase D Overexpression Reinforce the Histone Deacetylase 5 Redistribution in Heart Failure.
J. Bossuyt, K. Helmstadter, X. Wu, H. Clements-Jewery, R. S. Haworth, M. Avkiran, J. L. Martin, S. M. Pogwizd, and D. M. Bers (2008)
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Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection.
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Nucleic Acids Res.
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Prediction of Cancer Driver Mutations in Protein Kinases.
An RNA molecule that specifically inhibits G-protein-coupled receptor kinase 2 in vitro.
G. Mayer, B. Wulffen, C. Huber, J. Brockmann, B. Flicke, L. Neumann, D. Hafenbradl, B. M. Klebl, M. J. Lohse, C. Krasel, et al. (2008)
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Epigenetic inactivation of protein kinase D1 in gastric cancer and its role in gastric cancer cell migration and invasion.
M. Kim, H.-R. Jang, J.-H. Kim, S.-M. Noh, K.-S. Song, J.-S. Cho, H.-Y. Jeong, J. C. Norman, P. T. Caswell, G. H. Kang, et al. (2008)
Carcinogenesis
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Combination of Clk family kinase and SRp75 modulates alternative splicing of Adenovirus E1A..
J.-i. Yomoda, M. Muraki, N. Kataoka, T. Hosoya, M. Suzuki, M. Hagiwara, and H. Kimura (2008)
Genes Cells
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Protein-tyrosine Phosphatase {epsilon} Regulates Shc Signaling in a Kinase-specific Manner: INCREASING COHERENCE IN TYROSINE PHOSPHATASE SIGNALING.
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Characterization of Some Molecular Mechanisms Governing Autoactivation of the Catalytic Domain of the Anaplastic Lymphoma Kinase.
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Potassium Channel Phosphorylation in Excitable Cells: Providing Dynamic Functional Variability to a Diverse Family of Ion Channels.
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Sixteen-Kinase Gene Expression Identifies Luminal Breast Cancers with Poor Prognosis.
P. Finetti, N. Cervera, E. Charafe-Jauffret, C. Chabannon, C. Charpin, M. Chaffanet, J. Jacquemier, P. Viens, D. Birnbaum, and F. Bertucci (2008)
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Protein Kinase D in the Cardiovascular System: Emerging Roles in Health and Disease.
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Evolutionary Radiation Pattern of Novel Protein Phosphatases Revealed by Analysis of Protein Data from the Completely Sequenced Genomes of Humans, Green Algae, and Higher Plants.
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Plant Physiology
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Cyclic Nucleotide-dependent Protein Kinases Inhibit Binding of 14-3-3 to the GTPase-activating Protein Rap1GAP2 in Platelets.
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Transcriptional profiling of native inner medullary collecting duct cells from rat kidney.
P. Uawithya, T. Pisitkun, B. E. Ruttenberg, and M. A. Knepper (2008)
Physiol Genomics
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Activation of the SPS Amino Acid-Sensing Pathway in Saccharomyces cerevisiae Correlates with the Phosphorylation State of a Sensor Component, Ptr3.
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Identification of Functionally Distinct Regions That Mediate Biological Activity of the Protein Kinase A Homolog Tpk2.
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PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.
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Comparison of Miniaturized Time-Resolved Fluorescence Resonance Energy Transfer and Enzyme-Coupled Luciferase High-Throughput Screening Assays to Discover Inhibitors of Rho-Kinase II (ROCK-II).
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Gas6 and the Tyro 3 receptor tyrosine kinase subfamily regulate the phagocytic function of Sertoli cells.
W. Xiong, Y. Chen, H. Wang, H. Wang, H. Wu, Q. Lu, and D. Han (2008)
Reproduction
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PhosphoBlast, a Computational Tool for Comparing Phosphoprotein Signatures among Large Datasets.
Epidermal Growth Factor Receptor Phosphorylates Protein Kinase C {delta} at Tyr332 to form a Trimeric Complex with p66Shc in the H2O2-stimulated Cells.
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Modulation of F-actin Rearrangement by the Cyclic AMP/cAMP-dependent Protein Kinase (PKA) Pathway Is Mediated by MAPK-activated Protein Kinase 5 and Requires PKA-induced Nuclear Export of MK5.
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A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases.
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The Ste20-like kinase SvkA of Dictyostelium discoideum is essential for late stages of cytokinesis.
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Role for KAP1 Serine 824 Phosphorylation and Sumoylation/Desumoylation Switch in Regulating KAP1-mediated Transcriptional Repression.
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282, 36177-36189
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Expression of Serine/Threonine Protein-Kinases and Related Factors in Normal Monkey and Human Retinas: The Mechanistic Understanding of a CDK2 Inhibitor Induced Retinal Toxicity.
G. Saturno, M. Pesenti, C. Cavazzoli, A. Rossi, A. M. Giusti, B. Gierke, M. Pawlak, and M. Venturi (2007)
Toxicol Pathol
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Genetic Alterations in the Tyrosine Kinase Transcriptome of Human Cancer Cell Lines.
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Cancer Res.
67, 11368-11376
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Renal Cell Carcinoma: New Developments in Molecular Biology and Potential for Targeted Therapies.
Chemical Genetics Define the Roles of p38{alpha} and p38 in Acute and Chronic Inflammation.
S. J. O'Keefe, J. S. Mudgett, S. Cupo, J. N. Parsons, N. A. Chartrain, C. Fitzgerald, S.-L. Chen, K. Lowitz, C. Rasa, D. Visco, et al. (2007)
J. Biol. Chem.
282, 34663-34671
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A Novel Tyrosine Phosphorylation Site in Protein Kinase D Contributes to Oxidative Stress-mediated Activation.
Highly Efficient Phosphopeptide Enrichment by Calcium Phosphate Precipitation Combined with Subsequent IMAC Enrichment.
X. Zhang, J. Ye, O. N. Jensen, and P. Roepstorff (2007)
Mol. Cell. Proteomics
6, 2032-2042
|Abstract »|Full Text »|PDF »
Progressive loss of epidermal growth factor receptor in a subpopulation of breast cancers: implications in target-directed therapeutics.
L.-Y. Choong, S. Lim, M. C.-S. Loh, X. Man, Y. Chen, W. Toy, M. Pan, C.-S. Chen, A. Poonepalli, M. P. Hande, et al. (2007)
Mol. Cancer Ther.
6, 2828-2842
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Properties, Regulation, and in Vivo Functions of a Novel Protein Kinase D: CAENORHABDITIS ELEGANS DKF-2 LINKS DIACYLGLYCEROL SECOND MESSENGER TO THE REGULATION OF STRESS RESPONSES AND LIFE SPAN.
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282, 31273-31288
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Signalling through kinase-defective domains: the prevalence of atypical receptor-like kinases in plants.
Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain.
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PNAS
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Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics.
From the Cover: Structural basis for the specific inhibition of protein kinase G, a virulence factor of Mycobacterium tuberculosis.
N. Scherr, S. Honnappa, G. Kunz, P. Mueller, R. Jayachandran, F. Winkler, J. Pieters, and M. O. Steinmetz (2007)
PNAS
104, 12151-12156
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KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.
CCR Drug Updates: Sorafenib and Sunitinib in Renal Cell Carcinoma.
M. N. Stein and K. T. Flaherty (2007)
Clin. Cancer Res.
13, 3765-3770
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A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia.
T.-l. Gu, T. Mercher, J. W. Tyner, V. L. Goss, D. K. Walters, M. G. Cornejo, C. Reeves, L. Popova, K. Lee, M. C. Heinrich, et al. (2007)
Blood
110, 323-333
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c-Fms Tyrosine 559 Is a Major Mediator of M-CSF-induced Proliferation of Primary Macrophages.
S. Takeshita, R. Faccio, J. Chappel, L. Zheng, X. Feng, J. D. Weber, S. L. Teitelbaum, and F. P. Ross (2007)
J. Biol. Chem.
282, 18980-18990
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Intrinsic Fluctuations, Robustness, and Tunability in Signaling Cycles.
An Orally Available Small-Molecule Inhibitor of c-Met, PF-2341066, Exhibits Cytoreductive Antitumor Efficacy through Antiproliferative and Antiangiogenic Mechanisms.
H. Y. Zou, Q. Li, J. H. Lee, M. E. Arango, S. R. McDonnell, S. Yamazaki, T. B. Koudriakova, G. Alton, J. J. Cui, P.-P. Kung, et al. (2007)
Cancer Res.
67, 4408-4417
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Getting connected: analysis and principles of biological networks.
A Network-based Analysis of Polyanion-binding Proteins Utilizing Human Protein Arrays.
N. Salamat-Miller, J. Fang, C. W. Seidel, Y. Assenov, M. Albrecht, and C. R. Middaugh (2007)
J. Biol. Chem.
282, 10153-10163
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The Serine/Threonine/Tyrosine Phosphoproteome of the Model Bacterium Bacillus subtilis.
B. Macek, I. Mijakovic, J. V. Olsen, F. Gnad, C. Kumar, P. R. Jensen, and M. Mann (2007)
Mol. Cell. Proteomics
6, 697-707
|Abstract »|Full Text »|PDF »
Protein Kinase D Selectively Targets Cardiac Troponin I and Regulates Myofilament Ca2+ Sensitivity in Ventricular Myocytes.
F. Cuello, S. C. Bardswell, R. S. Haworth, X. Yin, S. Lutz, T. Wieland, M. Mayr, J. C. Kentish, and M. Avkiran (2007)
Circ. Res.
100, 864-873
|Abstract »|Full Text »|PDF »
The DNA-Dependent Protein Kinase Catalytic Subunit Is Phosphorylated In Vivo on Threonine 3950, a Highly Conserved Amino Acid in the Protein Kinase Domain.
P. Douglas, X. Cui, W. D. Block, Y. Yu, S. Gupta, Q. Ding, R. Ye, N. Morrice, S. P. Lees-Miller, and K. Meek (2007)
Mol. Cell. Biol.
27, 1581-1591
|Abstract »|Full Text »|PDF »
Proteomics Analysis of Protein Kinases by Target Class-selective Prefractionation and Tandem Mass Spectrometry.
J. Wissing, L. Jansch, M. Nimtz, G. Dieterich, R. Hornberger, G. Keri, J. Wehland, and H. Daub (2007)
Mol. Cell. Proteomics
6, 537-547
|Abstract »|Full Text »|PDF »
The Alliance for Cellular Signaling Plasmid Collection: A Flexible Resource for Protein Localization Studies and Signaling Pathway Analysis.
J. R. Zavzavadjian, S. Couture, W. S. Park, J. Whalen, S. Lyon, G. Lee, E. Fung, Q. Mi, J. Liu, E. Wall, et al. (2007)
Mol. Cell. Proteomics
6, 413-424
|Abstract »|Full Text »|PDF »
Cutting Edge: IL-1 Receptor-Associated Kinase 4 Structures Reveal Novel Features and Multiple Conformations.
A. Kuglstatter, A. G. Villasenor, D. Shaw, S. W. Lee, S. Tsing, L. Niu, K. W. Song, J. W. Barnett, and M. F. Browner (2007)
J. Immunol.
178, 2641-2645
|Abstract »|Full Text »|PDF »
Molecular basis for specificity in the druggable kinome: sequence-based analysis.
Meeting Report: Targeting the Kinome--20 Years of Tyrosine Kinase Inhibitor Research in Basel.
L. Bozulic, P. J. Morin, T. Hunter, and B. A. Hemmings (2007)
Sci. STKE
2007, pe8
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TFE3 Fusions Activate MET Signaling by Transcriptional Up-regulation, Defining Another Class of Tumors as Candidates for Therapeutic MET Inhibition.
M. Tsuda, I. J. Davis, P. Argani, N. Shukla, G. G. McGill, M. Nagai, T. Saito, M. Lae, D. E. Fisher, and M. Ladanyi (2007)
Cancer Res.
67, 919-929
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Synthesis and Characterization of 5'-p-fluorosulfonylbenzoyl-2' (or 3')-(biotinyl)adenosine as an Activity-Based Probe for Protein Kinases.
S. J. Ratcliffe, T. Yi, and S. S. Khandekar (2007)
J Biomol Screen
12, 126-132
|Abstract »|PDF »
The Rice Kinase Database. A Phylogenomic Database for the Rice Kinome.
C. Dardick, J. Chen, T. Richter, S. Ouyang, and P. Ronald (2007)
Plant Physiology
143, 579-586
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Large-scale phosphorylation analysis of mouse liver.
J. Villen, S. A. Beausoleil, S. A. Gerber, and S. P. Gygi (2007)
PNAS
104, 1488-1493
|Abstract »|Full Text »|PDF »
The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module.
N. Kannan, N. Haste, S. S. Taylor, and A. F. Neuwald (2007)
PNAS
104, 1272-1277
|Abstract »|Full Text »|PDF »
Role of protein O-linked N-acetyl-glucosamine in mediating cell function and survival in the cardiovascular system.
N. Fulop, R. B. Marchase, and J. C. Chatham (2007)
Cardiovasc Res
73, 288-297
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The first armadillo repeat is involved in the recognition and regulation of beta-catenin phosphorylation by protein kinase CK1.
V. H. Bustos, A. Ferrarese, A. Venerando, O. Marin, J. E. Allende, and L. A. Pinna (2006)
PNAS
103, 19725-19730
|Abstract »|Full Text »|PDF »
Comparison of Kinome Profiles of Barrett's Esophagus with Normal Squamous Esophagus and Normal Gastric Cardia.
J. W.P.M. van Baal, S. H. Diks, R. J.A. Wanders, A. M. Rygiel, F. Milano, J. Joore, J. J.G.H.M. Bergman, M. P. Peppelenbosch, and K. K. Krishnadath (2006)
Cancer Res.
66, 11605-11612
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Inhibition of Cell Migration by Autophosphorylated Mammalian Sterile 20-Like Kinase 3 (MST3) Involves Paxillin and Protein-tyrosine Phosphatase-PEST.
T.-J. Lu, W.-Y. Lai, C.-Y. F. Huang, W.-J. Hsieh, J.-S. Yu, Y.-J. Hsieh, W.-T. Chang, T.-H. Leu, W.-C. Chang, W.-J. Chuang, et al. (2006)
J. Biol. Chem.
281, 38405-38417
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Uses for JNK: the Many and Varied Substrates of the c-Jun N-Terminal Kinases.
M. A. Bogoyevitch and B. Kobe (2006)
Microbiol. Mol. Biol. Rev.
70, 1061-1095
|Abstract »|Full Text »|PDF »
A Microfluidics-Based Mobility Shift Assay to Discover New Tyrosine Phosphatase Inhibitors.
D. Perrin, C. Fremaux, D. Besson, W. H. Sauer, and A. Scheer (2006)
J Biomol Screen
11, 996-1004
|Abstract »|PDF »
Demonstration of a Genetic Therapeutic Index for Tumors Expressing Oncogenic BRAF by the Kinase Inhibitor SB-590885.