Journal ArticleDOI
The Protein Kinase Complement of the Human Genome
TLDR
The protein kinase complement of the human genome is catalogued using public and proprietary genomic, complementary DNA, and expressed sequence tag sequences to provide a starting point for comprehensive analysis of protein phosphorylation in normal and disease states and a detailed view of the current state of human genome analysis through a focus on one large gene family.Abstract:
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 protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.read more
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Mechanisms of TGF-β Signaling from Cell Membrane to the Nucleus
Yigong Shi,Joan Massagué +1 more
TL;DR: Current understanding on the mechanisms of TGF-β signaling from cell membrane to the nucleus is presented and the transcriptional regulation of target gene expression is reviewed.
Journal ArticleDOI
Activating mutation in the tyrosine kinase JAK2 in polycythemia vera, essential thrombocythemia, and myeloid metaplasia with myelofibrosis.
Ross L. Levine,Ross L. Levine,Martha Wadleigh,Jan Cools,Benjamin L. Ebert,Benjamin L. Ebert,Gerlinde Wernig,Brian J. P. Huntly,Titus J. Boggon,Iwona Wlodarska,Jennifer J. Clark,Sandra A. Moore,Jennifer Adelsperger,Sumin Koo,Jeffrey C. Lee,Stacey Gabriel,Thomas Mercher,Alan D. D'Andrea,Stefan Fröhling,Konstanze Döhner,Peter Marynen,Peter Vandenberghe,Ruben A. Mesa,Ayalew Tefferi,James D. Griffin,Michael J. Eck,William R. Sellers,William R. Sellers,Matthew Meyerson,Matthew Meyerson,Todd R. Golub,Todd R. Golub,Todd R. Golub,Stephanie J. Lee,D. Gary Gilliland,D. Gary Gilliland,D. Gary Gilliland +36 more
TL;DR: High-throughput DNA resequencing identified a recurrent somatic missense mutation JAK2V617F in granulocyte DNA samples of 121 of 164 PV patients, of which 41 had homozygous and 80 had heterozygous mutations.
Journal Article
Patterns of Somatic Mutation in Human Cancer Genomes
TL;DR: In this paper, the coding exons of the family of 518 protein kinases were sequenced in 210 cancers of diverse histological types to explore the nature of the information that will be derived from cancer genome sequencing.
Journal ArticleDOI
Patterns of somatic mutation in human cancer genomes
Christopher Greenman,Philip J. Stephens,Raffaella Smith,Gillian L. Dalgliesh,Christopher I. Hunter,Graham R. Bignell,Helen Davies,Jon W. Teague,Adam Butler,Claire Stevens,Sarah Edkins,Sarah O’Meara,Imre Vastrik,Esther Schmidt,Tim Avis,Syd Barthorpe,Gurpreet Bhamra,Gemma Buck,Bhudipa Choudhury,Jody Clements,Jennifer Cole,Ed Dicks,Simon A. Forbes,Kris Gray,Kelly Halliday,Rachel Harrison,Katy Hills,Jon Hinton,Andy Jenkinson,David T. Jones,Andy Menzies,Tatiana Mironenko,Janet Perry,Keiran Raine,Dave Richardson,Rebecca Shepherd,Alexandra Small,Calli Tofts,Jennifer Varian,Tony Webb,Sofie West,Sara Widaa,Andrew D. Yates,Daniel P. Cahill,David N. Louis,Peter Goldstraw,Andrew G. Nicholson,Francis Brasseur,Leendert H. J. Looijenga,Barbara L. Weber,Yoke Eng Chiew,Anna deFazio,Mel Greaves,Anthony R. Green,Peter J. Campbell,Ewan Birney,Douglas F. Easton,Georgia Chenevix-Trench,Min-Han Tan,Sok Kean Khoo,Bin Tean Teh,Siu Tsan Yuen,Suet Yi Leung,Richard Wooster,P. Andrew Futreal,Michael R. Stratton,Michael R. Stratton +66 more
TL;DR: More than 1,000 somatic mutations found in 274 megabases of DNA corresponding to the coding exons of 518 protein kinase genes in 210 diverse human cancers reveal the evolutionary diversity of cancers and implicates a larger repertoire of cancer genes than previously anticipated.
Journal ArticleDOI
Mechanism of Activation of the Raf-Erk Signaling Pathway by Oncogenic Mutations of B-Raf
Paul T C Wan,Mathew J. Garnett,S. Mark Roe,Sharlene Lee,Dan Niculescu-Duvaz,Valerie M. Good,Cancer Genome,C. Michael Jones,Christopher J. Marshall,Caroline J. Springer,David Barford,Richard Marais +11 more
TL;DR: The high activity mutants signal to ERK by directly phosphorylating MEK, whereas the impaired activity mutants stimulate MEK by activating endogenous C-RAF, possibly via an allosteric or transphosphorylation mechanism.
References
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
The sequence of the human genome.
J. Craig Venter,Mark Raymond Adams,Eugene W. Myers,Peter W. Li,Richard J. Mural,Granger G. Sutton,Hamilton O. Smith,Mark Yandell,Cheryl A. Evans,Robert A. Holt,Jeannine D. Gocayne,Peter Amanatides,Richard M. Ballew,Daniel H. Huson,Jennifer R. Wortman,Qing Zhang,Chinnappa D. Kodira,Xiangqun H. Zheng,Lin Chen,Marian P. Skupski,Gangadharan Subramanian,Paul Thomas,Jinghui Zhang,George L. Gabor Miklos,Catherine R. Nelson,Samuel Broder,Andrew G. Clark,J. H. Nadeau,Victor A. McKusick,Norton D. Zinder,Arnold J. Levine,Richard J. Roberts,M. I. Simon,Carolyn W. Slayman,Michael W. Hunkapiller,Randall Bolanos,Arthur L. Delcher,Ian M. Dew,Daniel Fasulo,Michael Flanigan,Liliana Florea,Aaron L. Halpern,Sridhar Hannenhalli,Saul A. Kravitz,Samuel Levy,Clark M. Mobarry,Knut Reinert,Karin A. Remington,Jane Abu-Threideh,Ellen M. Beasley,Kendra Biddick,Vivien Bonazzi,Rhonda Brandon,Michele Cargill,Ishwar Chandramouliswaran,Rosane Charlab,Kabir Chaturvedi,Zuoming Deng,Valentina Di Francesco,Patrick Dunn,Karen Eilbeck,Carlos Evangelista,Andrei Gabrielian,Weiniu Gan,Wangmao Ge,Fangcheng Gong,Zhiping Gu,Ping Guan,Thomas J. Heiman,Maureen E. Higgins,Rui-Ru Ji,Zhaoxi Ke,Karen A. Ketchum,Zhongwu Lai,Yiding Lei,Zhenya Li,Jiayin Li,Yong Liang,Xiaoying Lin,Fu Lu,Gennady V. Merkulov,Natalia Milshina,Helen M. Moore,Ashwinikumar K Naik,Vaibhav A. Narayan,Beena Neelam,Deborah Nusskern,Douglas B. Rusch,Steven L. Salzberg,Wei Shao,Bixiong Chris Shue,Jingtao Sun,Zhen Yuan Wang,Aihui Wang,Xin Wang,Jian Wang,Ming-Hui Wei,Ron Wides,Chunlin Xiao,Chunhua Yan,Alison Yao,Jane Ye,Ming Zhan,Weiqing Zhang,Hongyu Zhang,Qi Zhao,Liansheng Zheng,Fei Zhong,Wenyan Zhong,Shiaoping C. Zhu,Shaying Zhao,Dennis A. Gilbert,Suzanna Baumhueter,Gene Spier,Christine Carter,Anibal Cravchik,Trevor Woodage,Feroze Ali,Huijin An,Aderonke Awe,Danita Baldwin,Holly Baden,Mary Barnstead,Ian Barrow,Karen Beeson,Dana A. Busam,Amy Carver,Ming Lai Cheng,Liz Curry,Steve Danaher,Lionel Davenport,Raymond Desilets,Susanne Dietz,Kristina Dodson,Lisa Doup,Steven Ferriera,Neha Garg,Andres Gluecksmann,Brit J. Hart,Jason Haynes,Charles Haynes,Cheryl Heiner,Suzanne Hladun,Damon Hostin,Jarrett Houck,Timothy Howland,Chinyere Ibegwam,Jeffery Johnson,Francis Kalush,Lesley Kline,Shashi Koduru,Amy Love,Felecia Mann,David May,Steven McCawley,Tina C. McIntosh,Ivy McMullen,Mee Moy,Linda Moy,Brian Murphy,Keith Nelson,Cynthia Pfannkoch,Eric Pratts,Vinita Puri,Hina Qureshi,Matthew Reardon,Robert Rodriguez,Yu-Hui Rogers,Deanna Romblad,Bob Ruhfel,Richard T. Scott,Cynthia Sitter,Michelle Smallwood,Erin Stewart,Renee Strong,Ellen Suh,Reginald Thomas,Ni Ni Tint,Sukyee Tse,Claire Vech,Gary Wang,Jeremy Wetter,Sherita Williams,Monica Williams,Sandra Windsor,Emily Winn-Deen,Keriellen Wolfe,Jayshree Zaveri,Karena Zaveri,Josep F. Abril,Roderic Guigó,Michael J. Campbell,Kimmen Sjölander,Brian Karlak,Anish Kejariwal,Huaiyu Mi,Betty Lazareva,Thomas Hatton,Apurva Narechania,Karen Diemer,Anushya Muruganujan,Nan Guo,Shinji Sato,Vineet Bafna,Sorin Istrail,Ross Lippert,Russell Schwartz,Brian P. Walenz,Shibu Yooseph,David Allen,Anand Basu,James Baxendale,Louis Blick,Marcelo Caminha,John Carnes-Stine,Parris Caulk,Yen-Hui Chiang,My Coyne,Carl Dahlke,Anne Deslattes Mays,Maria Dombroski,Michael Donnelly,Dale Ely,Shiva Esparham,Carl Fosler,Harold Gire,Stephen Glanowski,Kenneth Glasser,Anna Glodek,Mark Gorokhov,Ken Graham,Barry Gropman,Michael Harris,Jeremy Heil,Scott Henderson,Jeffrey Hoover,Donald Jennings,Catherine Jordan,James Jordan,John Kasha,Leonid Kagan,Cheryl L. Kraft,Alexander Levitsky,Mark Lewis,Xiangjun Liu,John Lopez,Daniel Ma,William H. Majoros,Joe McDaniel,Sean C. Murphy,Matthew Newman,Trung Hieu Nguyen,Ngoc Nguyen,Marc Nodell,Sue Pan,Jim Peck,Marshall Peterson,William Rowe,Robert Sanders,John Scott,Michael Simpson,Thomas J. Smith,Arlan Sprague,Timothy B. Stockwell,Russell Turner,Eli Venter,Mei Wang,Meiyuan Wen,David Wu,Mitchell Wu,Ashley Xia,Ali Zandieh,Xiaohong Zhu +272 more
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Journal ArticleDOI
Oncogenic kinase signalling
Peter Blume-Jensen,Tony Hunter +1 more
TL;DR: How oncogenic conversion of protein kinases results from perturbation of the normal autoinhibitory constraints on kinase activity is emphasized and an update is provided on the role of deregulated PI(3)K/Akt and mammalian target of rapamycin/p70S6K signalling in human malignancies.
Journal ArticleDOI
Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification.
Steven K. Hanks,Tony Hunter +1 more
TL;DR: The eukaryotic protein kinases make up a large superfamily of homologous proteins, and a classification scheme can be founded on a kinase domain phylogeny, which reveals families of enzymes that have related substrate specificities and modes of regulation.
Journal ArticleDOI
Signaling--2000 and beyond.
TL;DR: The important findings in the history of signal transduction are adequately covered in many reviews, and I have therefore cited reviews that discuss the seminal papers.
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Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification.
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