A functional network of yeast genes using gene ontology information

Erliang Zeng, Giri Narasimhan, Lisa Schneper, Kalai Mathee

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

Abstract

In the post-genomic era, the organization of genes into networks has played an important role in characterizing the functions of individual genes and the interplay between them. It is also vital in understanding complex cellular processes and their dynamics. Despite advances, gene network prediction still remains a challenge. Recently, heterogeneous genomic and proteomic data were integrated to generate a functional network of yeast genes. The Gene Ontology (GO) project has integrated information from multiple data sources to annotate genes to specific biological process. Generating gene networks using GO annotations is a novel and alternative way to efficiently integrate heterogeneous data sources. In this paper, we present a novel approach to automatically generate a functional network of yeast genes using Gene Ontology (GO) annotations. An information theoretic semantic similarity (SS) was calculated between every pair of genes based on the method proposed by Resnik. This SS score was then used to predict linkages between genes, to generate a functional network. An alternative approach has been proposed using a measure called log likelihood score (LLS). The Functional networks predicted using the SS and LLS measures were compared. We discussed our experiments on generating reliable functional gene networks and concluded that the functional network generated by SS scores is comparable to or better than those obtained using LLS scores.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages343-346
Number of pages4
DOIs
StatePublished - Dec 1 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

Fingerprint

Gene Ontology
Gene Regulatory Networks
Yeast
Ontology
Genes
Yeasts
Semantics
Molecular Sequence Annotation
Information Storage and Retrieval
Biological Phenomena
Proteomics

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

Cite this

Zeng, E., Narasimhan, G., Schneper, L., & Mathee, K. (2008). A functional network of yeast genes using gene ontology information. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 (pp. 343-346). [4684916] (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.60
Zeng, Erliang ; Narasimhan, Giri ; Schneper, Lisa ; Mathee, Kalai. / A functional network of yeast genes using gene ontology information. Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. pp. 343-346 (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).
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Zeng, E, Narasimhan, G, Schneper, L & Mathee, K 2008, A functional network of yeast genes using gene ontology information. in Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008., 4684916, Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, pp. 343-346, 2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, Philadelphia, PA, United States, 11/3/08. https://doi.org/10.1109/BIBM.2008.60

A functional network of yeast genes using gene ontology information. / Zeng, Erliang; Narasimhan, Giri; Schneper, Lisa; Mathee, Kalai.

Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 343-346 4684916 (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).

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

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Zeng E, Narasimhan G, Schneper L, Mathee K. A functional network of yeast genes using gene ontology information. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 343-346. 4684916. (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.60