The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment
- Sean M. Grimmond1,5,
- Kevin C. Miranda1,5,
- Zheng Yuan1,
- Melissa J. Davis1,
- David A. Hume1,
- Ken Yagi2,
- Naoko Tominaga2,
- Hidemasa Bono2,
- Yoshihide Hayashizaki2,3,
- Yasushi Okazaki2,3,
- RIKEN GER Group2,
- GSL Members3,4, and
- Rohan D. Teasdale1,6
- 1Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St. Lucia 4072, Australia
- 2Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- 3Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan
Abstract
We have developed a computational strategy to identify the set of soluble proteins secreted into the extracellular environment of a cell. Within the protein sequences predominantly derived from the RIKEN representative transcript and protein set, we identified 2033 unique soluble proteins that are potentially secreted from the cell. These proteins contain a signal peptide required for entry into the secretory pathway and lack any transmembrane domains or intracellular localization signals. This class of proteins, which we have termed the mouse secretome, included >500 novel proteins and 92 proteins <100 amino acids in length. Functional analysis of the secretome included identification of human orthologs, functional units based on InterPro and SCOP Superfamily predictions, and expression of the proteins within the RIKEN READ microarray database. To highlight the utility of this information, we discuss the CUB domain-containing protein family.
Footnotes
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[Supplemental material is available at www.genome.org.]
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.983703.
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↵5 These authors contributed equally to this work.
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↵4 Takahiro Arakawa, Piero Carninci, and Jun Kawai.
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↵6 Corresponding author. E-MAIL R.Teasdale{at}imb.uq.edu.au; FAX 61-7-3346-2101.
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- Accepted April 17, 2003.
- Received December 3, 2002.
- Cold Spring Harbor Laboratory Press
