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Letter

Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse

¹The Institute for Molecular Bioscience, Australia ²University of Queensland, Queensland, Australia ³The Australian Research Council Special Research Centre for Functional and Applied Genomics, University of Queensland, Queensland, Australia ⁴Cooperative Research Centre for Chronic Inflammatory Disease, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-Ku, Yokohama, Kanagawa, 230-0045, Japan ⁵Computational Biology and Bioinformatics Environment ComBinE, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-Ku, Yokohama, Kanagawa, 230-0045, Japan ⁶Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-Ku, Yokohama, Kanagawa, 230-0045, Japan ⁷Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan

With the completion of the human and mouse genome sequences, the task now turns to identifying their encoded transcripts and assigning gene function. In this study, we have undertaken a computational approach to identify and classify all of the protein kinases and phosphatases present in the mouse gene complement. A nonredundant set of these sequences was produced by mining Ensembl gene predictions and publicly available cDNA sequences with a panel of InterPro domains. This approach identified 561 candidate protein kinases and 162 candidate protein phosphatases. This cohort was then analyzed using TribeMCL protein sequence similarity clustering followed by CLUSTALV alignment and hierarchical tree generation. This approach allowed us to (1) distinguish between true members of the protein kinase and phosphatase families and enzymes of related biochemistry, (2) determine the structure of the families, and (3) suggest functions for previously uncharacterized members. The classifications obtained by this approach were in good agreement with previous schemes and allowed us to demonstrate domain associations with a number of clusters. Finally, we comment on the complementary nature of cDNA and genome-based gene detection and the impact of the FANTOM2 transcriptome project.

⁹ Corresponding author.
E-MAIL a.forrest{at}imb.uq.edu.au; FAX 61-7-3365 4388.

⁸ Takahiro Arakawa, Piero Carninci, Jun Kawai, and Yoshihide Hayashizaki.

[Supplemental material is available online at www.genome.org.]

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