Skip Navigation


Bioinformatics Advance Access originally published online on July 4, 2006
Bioinformatics 2006 22(16):2037-2043; doi:10.1093/bioinformatics/btl345
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
22/16/2037    most recent
btl345v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (3)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Li, J.
Right arrow Articles by Galbraith, D. W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, J.
Right arrow Articles by Galbraith, D. W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A framework of integrating gene relations from heterogeneous data sources: an experiment on Arabidopsis thaliana

Jiexun Li 1,*, Xin Li 1, Hua Su 1, Hsinchun Chen 1 and David W. Galbraith 2

1 Department of Management Information Systems, University of Arizona Tucson, AZ 85721, USA
2 Department of Plant Sciences, University of Arizona Tucson, AZ 85721, USA

*To whom correspondence should be addressed.


  Abstract

One of the most important goals of biological investigation is to uncover gene functional relations. In this study we propose a framework for extraction and integration of gene functional relations from diverse biological data sources, including gene expression data, biological literature and genomic sequence information. We introduce a two-layered Bayesian network approach to integrate relations from multiple sources into a genome-wide functional network. An experimental study was conducted on a test-bed of Arabidopsis thaliana. Evaluation of the integrated network demonstrated that relation integration could improve the reliability of relations by combining evidence from different data sources. Domain expert judgments on the gene functional clusters in the network confirmed the validity of our approach for relation integration and network inference.

Contact: jiexun{at}eller.arizona.edu

Associate Editor: Martin Bishop

Received on April 19, 2006; revised on June 16, 2006; accepted on June 22, 2006

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
A. Lysenko, M. M. Hindle, J. Taubert, M. Saqi, and C. J. Rawlings
Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases
Brief Bioinform, November 1, 2009; 10(6): 676 - 693.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Z. Tian, T. Hwang, and R. Kuang
A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge
Bioinformatics, November 1, 2009; 25(21): 2831 - 2838.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
A. Krishnan and A. Pereira
Integrative approaches for mining transcriptional regulatory programs in Arabidopsis
Brief Funct Genomic Proteomic, July 16, 2008; (2008) eln035v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Cui, P. Li, G. Li, F. Xu, C. Zhao, Y. Li, Z. Yang, G. Wang, Q. Yu, Y. Li, et al.
AtPID: Arabidopsis thaliana protein interactome database an integrative platform for plant systems biology
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D999 - D1008.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.