Mouse Proteome Analysis

  1. Alexander Kanapin1,11,
  2. Serge Batalov4,
  3. Melissa J. Davis3,
  4. Julian Gough5,
  5. Sean Grimmond3,
  6. Hideya Kawaji2,8,
  7. Michele Magrane1,
  8. Hideo Matsuda2,
  9. Christian Schönbach6,
  10. Rohan D. Teasdale3,
  11. RIKEN GER Group7,
  12. GSL Members9,10, and
  13. Zheng Yuan3
  1. 1EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
  2. 2Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka 560-8531, Japan
  3. 3Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St. Lucia, Queensland 4072, Australia
  4. 4Genomic Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA
  5. 5Department of Structural Biology, Stanford University, Stanford, California 94305, USA
  6. 6Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
  7. 7Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
  8. 8NTT Software Corporation, Naka-ku, Yokohama, Kanagawa, 231-8554, Japan
  9. 9Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan

Abstract

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

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.978703.

  • 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.

    • Accepted March 5, 2003.
    • Received November 11, 2002.
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