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Integration of genomic datasets to predict protein complexes in yeast

  • Ronald Jansen
  • Ning Lan
  • Jiang Qian
  • Mark Gerstein
Article

Abstract

The ultimate goal of functional genomics is to define the function of all the genes in the genome of an organism. A large body of information of the biological roles of genes has been accumulated and aggregated in the past decades of research, both from traditional experiments detailing the role of individual genes and proteins, and from newer experimental strategies that aim to characterize gene function on a genomic scale.

It is clear that the goal of functional genomics can only be achieved by integrating information and data sources from the variety of these different experiments. Integration of different data is thus an important challenge for bioinformatics.

The integration of different data sources often helps to uncover non-obvious relationships between genes, but there are also two further benefits. First, it is likely that whenever information from multiple independent sources agrees, it should be more valid and reliable. Secondly, by looking at the union of multiple sources, one can cover larger parts of the genome. This is obvious for integrating results from multiple single gene or protein experiments, but also necessary for many of the results from genome-wide experiments since they are often confined to certain (although sizable) subsets of the genome.

In this paper, we explore an example of such a data integration procedure. We focus on the prediction of membership in protein complexes for individual genes. For this, we recruit six different data sources that include expression profiles, interaction data, essentiality and localization information. Each of these data sources individually contains some weakly predictive information with respect to protein complexes, but we show how this prediction can be improved by combining all of them. Supplementary information is available at http://bioinfo.mbb.yale.edu/integrate/interactions/.Abbreviations: TP: true possitive; TN: true negative; FP: false positive; FN: false negative; Y2H: yeast two-hybrid.

Keywords

Protein Complex Localization Information Supplementary Information Individual Gene Biological Role 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Ronald Jansen
    • 1
  • Ning Lan
    • 1
  • Jiang Qian
    • 1
  • Mark Gerstein
    • 2
  1. 1.Department of Molecular Biophysics & BiochemistryYale UniversityNew HavenUSA
  2. 2.Department of Molecular Biophysics & Biochemistry and Computer ScienceYale UniversityNew HavenUSA

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