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Comparative Study
. 2003 Jun;13(6B):1335-44.
doi: 10.1101/gr.978703.

Mouse proteome analysis

Alexander Kanapin  1 , Serge Batalov, Melissa J Davis, Julian Gough, Sean Grimmond, Hideya Kawaji, Michele Magrane, Hideo Matsuda, Christian Schönbach, Rohan D Teasdale, Zheng Yuan; RIKEN GER Group; GSL Members
Affiliations
Comparative Study

Mouse proteome analysis

Alexander Kanapin et al. Genome Res. 2003 Jun.

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

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Figures

Figure 1
Figure 1
Comparative diagram of the GO Slim categories for different mouse and human proteomes. The y-axis indicates the number of proteins; the x-axis indicates the following GO categories: GO:0003676 nucleic_acid_binding; GO:0003754 chaperone; GO:0003774 motor; GO:0003793 defense/immunity_protein; GO:0003824 enzyme; GO:0004871 signal_transducer; GO:0005198 structural_molecule; GO:0005215 transporter; GO:0005488 binding; GO:0005554 molecular_function_unknown; GO:0015070 toxin; GO:0030234 enzyme_regulator; GO: 0030528 transcription_regulator.
Figure 2
Figure 2
Comparative diagram of the GO Slim categories for different eukaryotic proteomes. The y-axis shows the number of proteins; the x-axis shows GO categories (see Fig. 1).
Figure 3
Figure 3
Observed evolutionary domains. The ordered sizes of superfamilies with greater than 100 members.
Figure 4
Figure 4
Observed evolutionary domains. The distribution sizes of superfamilies with less than 100 members.
See this image and copyright information in PMC

References

    1. Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M.D., et al. 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29: 37-40. - PMC - PubMed
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    1. FANTOM Consortium 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573. - PubMed
    1. Gough, J. 2002. The superfamily database in structural genomics. Acta Crystallogr. D Biol. Crystallogr. 58: 1897-1900. - PubMed
    1. Gough, J. and Chothia, C. 2002. Superfamily: HMMs representing all proteins of known structure. Nucleic Acids Res. 30: 268-272. - PMC - PubMed

WEB SITE REFERENCES

    1. http://www.celeradiscoverysystem.com; Celera Corporation.
    1. http://www.ensembl.org/; ENSEMBL genome databases.
    1. http://www.ebi.ac.uk/IPI; International Protein Index.
    1. http://www.ebi.ac.uk/proteome; Proteome Analysis Database.
    1. http://genome.gsc.riken.go.jp/; RIKEN Mouse Representative Transcript and Protein Sets. - PubMed

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