Integrative protein function transfer using factor graphs and heterogeneous data sources

Antonina Mitrofanova, Vladimir Pavlovic, Bud Mishra

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We propose a novel approach for predicting protein functions of an organism by coupling sequence homology and PPI data between two (or more) species with multifunctional Gene Ontology information into a single computational model. Instead of using a network of one organism in isolation, we join networks of different species by inter-species sequence homology links of sufficient similarity. As a consequence, the knowledge of a protein's function is acquired not only from one species' network alone, but also through homologous links to the networks of different species. We apply our method to two largest protein networks, Yeast (Saccharomyces cerevisiae) and Fly (Drosophila melanogaster). Our joint Fly-Yeast network displays statistically significant improvements in precision, accuracy, and false positive rate over networks that consider either of the sources in isolation, while retaining the computational efficiency of the simpler models.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages314-318
Number of pages5
DOIs
StatePublished - 2008
Event2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States
Duration: Nov 3 2008Nov 5 2008

Publication series

NameProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Other

Other2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
CountryUnited States
CityPhiladelphia, PA
Period11/3/0811/5/08

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

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  • Cite this

    Mitrofanova, A., Pavlovic, V., & Mishra, B. (2008). Integrative protein function transfer using factor graphs and heterogeneous data sources. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 (pp. 314-318). [4684910] (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.65