Sun, 27 Jul 2008 07:24:41 BST CiteULike: neils's Suzuki http://www.citeulike.org/user/neils/author/Suzuki CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2709869 <i>Nature, Vol. 452, No. 7190. (24 April 2008), pp. 991-996.</i> The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Ray Ming Shaobin Hou Yun Feng Qingyi Yu Alexandre Dionne-Laporte Jimmy Saw Pavel Senin Wei Wang Benjamin Ly Kanako Lewis Steven Salzberg Lu Feng Meghan Jones Rachel Skelton Jan Murray Cuixia Chen Wubin Qian Junguo Shen Peng Du Moriah Eustice Eric Tong Haibao Tang Eric Lyons Robert Paull Todd Michael Kerr Wall Danny Rice Henrik Albert Ming-Li Wang Yun Zhu Michael Schatz Niranjan Nagarajan Ricelle Acob Peizhu Guan Andrea Blas Ching Wai Christine Ackerman Yan Ren Chao Liu Jianmei Wang Jianping Wang Jong-Kuk Na Eugene Shakirov Brian Haas Jyothi Thimmapuram David Nelson Xiyin Wang John Bowers Andrea Gschwend Arthur Delcher Ratnesh Singh Jon Suzuki Savarni Tripathi Kabi Neupane Hairong Wei Beth Irikura Maya Paidi Ning Jiang Wenli Zhang Gernot Presting Aaron Windsor Rafael Navajas-Perez Manuel Torres Alex Feltus Brad Porter Yingjun Li Max Burroughs Ming-Cheng Luo Lei Liu David Christopher Stephen Mount Paul Moore Tak Sugimura Jiming Jiang Mary Schuler Vikki Friedman Thomas Mitchell-Olds Dorothy Shippen Claude Depamphilis Jeffrey Palmer Michael Freeling Andrew Paterson Dennis Gonsalves Lei Wang Maqsudul Alam doi:10.1038/nature06856 Nature, Vol. 452, No. 7190. (24 April 2008), pp. 991-996. 2008-04-23T19:37:29-00:00 2008 Nature 452 7190 991 996 Nature Publishing Group genome genomics papaya plant sequence http://www.citeulike.org/user/neils/article/2278653 <i>Genome Biology, Vol. 9, No. 1. (2008)</i><br /><br />BACKGROUND:The nucleus is a complex cellular organelle and accurately defining its protein content is essential before any systematic characterisation can be considered. RESULTS:Here, we report direct evidence for 2568 mammalian proteins within the nuclear proteome: the nuclear subcellular localization of 1529 proteins based on a high-throughput subcellular localization protocol of full-length proteins and an additional 1039 proteins for which clear experimental evidence is documented in published literature. CONCLUSIONS:This represents direct experimental evidence that the nuclear proteome consists of at least 14% of the entire proteome. This high-quality nuclear proteome dataset was used to evaluate computational approaches designed to identify additional nuclear proteins. Based on this analysis researchers can determine the stringency and types of lines of evidence they consider to infer the size and complement of the nuclear proteome. Towards defining the nuclear proteome Lynn Fink Seetha Karunaratne Amit Mittal Donald Gardiner Nicholas Hamilton Donna Mahony Chikatoshi Kai Harukazu Suzuki Yosihide Hayashizaki Rohan Teasdale doi:10.1186/gb-2008-9-1-r15 Genome Biology, Vol. 9, No. 1. (2008) 2008-01-23T02:49:37-00:00 2008 Genome Biology 9 1 bioinformatics localisation nls nuclear proteome scl http://www.citeulike.org/user/neils/article/577046 <i>BMC Bioinformatics, Vol. 7 (2006)</i><br /><br />BACKGROUND: Protein kinases and protein phosphatases are the fundamental components of phosphorylation dependent protein regulatory systems. We have created a database for the protein kinase-like and phosphatase-like loci of mouse http://phosphoreg.imb.uq.edu.au that integrates protein sequence, interaction, classification and pathway information with the results of a systematic screen of their sub-cellular localization and tissue specific expression data mined from the GNF tissue atlas of mouse. RESULTS: The database lets users query where a specific kinase or phosphatase is expressed at both the tissue and sub-cellular levels. Similarly the interface allows the user to query by tissue, pathway or sub-cellular localization, to reveal which components are co-expressed or co-localized. A review of their expression reveals 30% of these components are detected in all tissues tested while 70% show some level of tissue restriction. Hierarchical clustering of the expression data reveals that expression of these genes can be used to separate the samples into tissues of related lineage, including 3 larger clusters of nervous tissue, developing embryo and cells of the immune system. By overlaying the expression, sub-cellular localization and classification data we examine correlations between class, specificity and tissue restriction and show that tyrosine kinases are more generally expressed in fewer tissues than serine/threonine kinases. CONCLUSION: Together these data demonstrate that cell type specific systems exist to regulate protein phosphorylation and that for accurate modelling and for determination of enzyme substrate relationships the co-location of components needs to be considered. PhosphoregDB: the tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. AR Forrest DF Taylor JL Fink MM Gongora C Flegg RD Teasdale H Suzuki M Kanamori C Kai Y Hayashizaki SM Grimmond doi:10.1186/1471-2105-7-82 BMC Bioinformatics, Vol. 7 (2006) 2006-04-05T13:54:19-00:00 2006 BMC Bioinformatics 1471-2105 7 database kinase phosphatase phosphorylation http://www.citeulike.org/user/neils/article/1302524 <i>Nature, Vol. 447, No. 7142., pp. 330-333.</i> Helicobacter pylori CagA targets PAR1/MARK kinase to disrupt epithelial cell polarity Iraj Saadat Hideaki Higashi Chikashi Obuse Mayumi Umeda Naoko Murata-Kamiya Yasuhiro Saito Huaisheng Lu Naomi Ohnishi Takeshi Azuma Atsushi Suzuki Shigeo Ohno Masanori Hatakeyama doi:10.1038/nature05765 Nature, Vol. 447, No. 7142., pp. 330-333. 2007-05-17T15:09:45-00:00 Nature 0028-0836 447 7142 330 333 Nature Publishing Group helicobacter kinase mark par1