Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals

M. Nakao; R.A. Barrero; Y. Mukai; C. Motono; M. Suwa; K. Nakai

doi:10.1093/nar/gki520

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Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals

Journal article

Open access

Peer reviewed

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals

M. Nakao, R.A. Barrero, Y. Mukai, C. Motono, M. Suwa and K. Nakai

Nucleic Acids Research, Vol.33(8), pp.2355-2363

2005

DOI: https://doi.org/10.1093/nar/gki520

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Abstract

We investigated human alternative protein isoforms of >2600 genes based on full-length cDNA clones and SwissProt. We classified the isoforms and examined their co-occurrence for each gene. Further, we investigated potential relationships between these changes and differential subcellular localization. The two most abundant patterns were the one with different C-terminal regions and the one with an internal insertion, which together account for 43% of the total. Although changes of the N-terminal region are less common than those of the C-terminal region, extension of the C-terminal region is much less common than that of the N-terminal region, probably because of the difficulty of removing stop codons in one isoform. We also found that there are some frequently used combinations of co-occurrence in alternative isoforms. We interpret this as evidence that there is some structural relationship which produces a repertoire of isoformal patterns. Finally, many terminal changes are predicted to cause differential subcellular localization, especially in targeting either peroxisomes or mitochondria. Our study sheds new light on the enrichment of the human proteome through alternative splicing and related events. Our database of alternative protein isoforms is available through the internet.

Details

Title: Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals
Authors/Creators: M. Nakao (Author/Creator) - The University of Tokyo
R.A. Barrero (Author/Creator)
Y. Mukai (Author/Creator)
C. Motono (Author/Creator)
M. Suwa (Author/Creator)
K. Nakai (Author/Creator)
Publication Details: Nucleic Acids Research, Vol.33(8), pp.2355-2363
Publisher: Oxford University Press
Identifiers: 991005543929107891
Copyright: © The Author 2005
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.469 Alternative Splicing
Web Of Science research areas: Biochemistry & Molecular Biology
ESI research areas: Biology & Biochemistry