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Database (Oxford). 2015 Aug 8;2015. pii: bav077. doi: 10.1093/database/bav077. Print 2015.

MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase.

Author information

1
Department of Computer Science and Information Systems, Center for Applied Chemical Biology and.
2
Center for Applied Chemical Biology and Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA.
3
Center for Applied Chemical Biology and Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA xmin@ysu.edu.

Abstract

The subcellular location of a protein is a key factor in determining the molecular function of the protein in an organism. MetazSecKB is a secretome and subcellular proteome knowledgebase specifically designed for metazoan, i.e. human and animals. The protein sequence data, consisting of over 4 million entries with 121 species having a complete proteome, were retrieved from UniProtKB. Protein subcellular locations including secreted and 15 other subcellular locations were assigned based on either curated experimental evidence or prediction using seven computational tools. The protein or subcellular proteome data can be searched and downloaded using several different types of identifiers, gene name or keyword(s), and species. BLAST search and community annotation of subcellular locations are also supported. Our primary analysis revealed that the proteome sizes, secretome sizes and other subcellular proteome sizes vary tremendously in different animal species. The proportions of secretomes vary from 3 to 22% (average 8%) in metazoa species. The proportions of other major subcellular proteomes ranged approximately 21-43% (average 31%) in cytoplasm, 20-37% (average 30%) in nucleus, 3-19% (average 12%) as plasma membrane proteins and 3-9% (average 6%) in mitochondria. We also compared the protein families in secretomes of different primates. The Gene Ontology and protein family domain analysis of human secreted proteins revealed that these proteins play important roles in regulation of human structure development, signal transduction, immune systems and many other biological processes. Database URL: http://proteomics.ysu.edu/secretomes/animal/index.php.

PMID:
26255309
PMCID:
PMC4529745
DOI:
10.1093/database/bav077
[Indexed for MEDLINE]
Free PMC Article

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