Use of Gene Ontology Annotation to understand the peroxisome proteome in humans

Database (Oxford). 2013 Jan 17;2013:bas062. doi: 10.1093/database/bas062. Print 2013.

Abstract

The Gene Ontology (GO) is the de facto standard for the functional description of gene products, providing a consistent, information-rich terminology applicable across species and information repositories. The UniProt Consortium uses both manual and automatic GO annotation approaches to curate UniProt Knowledgebase (UniProtKB) entries. The selection of a protein set prioritized for manual annotation has implications for the characteristics of the information provided to users working in a specific field or interested in particular pathways or processes. In this article, we describe an organelle-focused, manual curation initiative targeting proteins from the human peroxisome. We discuss the steps taken to define the peroxisome proteome and the challenges encountered in defining the boundaries of this protein set. We illustrate with the use of examples how GO annotations now capture cell and tissue type information and the advantages that such an annotation approach provides to users. Database URL: http://www.ebi.ac.uk/GOA/ and http://www.uniprot.org.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Humans
  • Molecular Sequence Annotation*
  • Organ Specificity
  • Peroxisomes / genetics
  • Peroxisomes / metabolism*
  • Protein Binding
  • Protein Interaction Mapping
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • Protein Transport
  • Proteome / genetics
  • Proteome / metabolism*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / metabolism
  • Species Specificity

Substances

  • Protein Isoforms
  • Proteome
  • Saccharomyces cerevisiae Proteins