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Scientific article
English

Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE

Contributors

Schuemie, Martijn; Chichester, Christine; Lisacek, Frédérique; Coute, Yohann; Roes, Peter-Jan; Sanchez, Jean-Charles; Kors, Jan; Mons, Barend

Published in

Proteomics, vol. 7, no. 6, p. 921-931

Publication date

2007

Abstract

Attribution of the most probable functions to proteins identified by proteomics is a significant challenge that requires extensive literature analysis. We have developed a system for automated prediction of implicit and explicit biologically meaningful functions for a proteomics study of the nucleolus. This approach uses a set of vocabulary terms to map and integrate the information from the entire MEDLINE database. Based on a combination of cross-species sequence homology searches and the corresponding literature, our approach facilitated the direct association between sequence data and information from biological texts describing function. Comparison of our automated functional assignment to manual annotation demonstrated our method to be highly effective. To establish the sensitivity, we defined the functional subtleties within a family containing a highly conserved sequence. Clustering of the DEAD-box protein family of RNA helicases confirmed that these proteins shared similar morphology although functional subfamilies were accurately identified by our approach. We visualized the nucleolar proteome in terms of protein functions using multi-dimensional scaling, showing functional associations between nucleolar proteins that were not previously realized. Finally, by clustering the functional properties of the established nucleolar proteins, we predicted novel nucleolar proteins. Subsequently, nonproteomics studies confirmed the predictions of previously unidentified nucleolar proteins.

Keywords

  • Amino Acid Sequence
  • Animals
  • DEAD-box RNA Helicases/chemistry/genetics/metabolism
  • Databases, Protein
  • Humans
  • MEDLINE
  • Molecular Sequence Data
  • Nuclear Proteins/chemistry/genetics/metabolism
  • Proteome

UNIGE affiliation entities

UNIGE research groups

Citation (ISO format)

SCHUEMIE, Martijn et al. Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE. In: Proteomics, 2007, vol. 7, n° 6, p. 921–931. doi: 10.1002/pmic.200600693

Main files (1)

Article (Published version)

Identifiers

Journal ISSN

1615-9853
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Technical informations

Creation

15/11/2013 11:00:00

First validation

15/11/2013 11:00:00

Update

09/01/2025 17:07:21

Status update

09/01/2025 17:07:21

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09/01/2025 17:11:40
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