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Letter

Mouse Proteome Analysis

¹EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK ²Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka 560-8531, Japan ³Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St. Lucia, Queensland 4072, Australia ⁴Genomic Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA ⁵Department of Structural Biology, Stanford University, Stanford, California 94305, USA ⁶Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan ⁷Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan ⁸NTT Software Corporation, Naka-ku, Yokohama, Kanagawa, 231-8554, Japan ⁹Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan

A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein sequences derived from a nonredundant representative protein set (RPS) and a variant protein set (VPS) of the mouse transcriptome. The functional characterization and assignment of Gene Ontology terms was done by analysis of the proteome using InterPro. The Superfamily database analyses gave a detailed structural classification according to SCOP and provide additional evidence for the functional characterization of the proteome data. The MDS database analysis revealed new domains which are not presented in existing protein domain databases. Thus the transcriptome gives us a unique source of data for the detection of new functional groups. The data obtained for the RPS and VPS sets facilitated the comparison of different patterns of protein expression. A comparison of other existing mouse and human protein sequence sets (e.g., the International Protein Index) demonstrates the common patterns in mammalian proteomes. The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins

¹¹ Corresponding author.
E-MAIL alex{at}ebi.ac.uk; FAX 44 0 1223 494610.

¹⁰ Takahiro Arakawa, Piero Carninci, Jun Kawai, and Yoshihide Hayashizaki.

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