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Bioinformatics Advance Access originally published online on November 16, 2006
Bioinformatics 2007 23(2):222-231; doi:10.1093/bioinformatics/btl581
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Network neighborhood analysis with the multi-node topological overlap measure

Ai Li 1 and Steve Horvath 1,2,*

1 Department of Biostatistics, School of Public Health, University of California Los Angeles, CA 90095-1772, USA
2 Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095-7088, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The goal of neighborhood analysis is to find a set of genes (the neighborhood) that is similar to an initial ‘seed’ set of genes. Neighborhood analysis methods for network data are important in systems biology. If individual network connections are susceptible to noise, it can be advantageous to define neighborhoods on the basis of a robust interconnectedness measure, e.g. the topological overlap measure. Since the use of multiple nodes in the seed set may lead to more informative neighborhoods, it can be advantageous to define multi-node similarity measures.

Results: The pairwise topological overlap measure is generalized to multiple network nodes and subsequently used in a recursive neighborhood construction method. A local permutation scheme is used to determine the neighborhood size. Using four network applications and a simulated example, we provide empirical evidence that the resulting neighborhoods are biologically meaningful, e.g. we use neighborhood analysis to identify brain cancer related genes.

Availability: An executable Windows program and tutorial for multi-node topological overlap measure (MTOM) based analysis can be downloaded from the webpage (http://www.genetics.ucla.edu/labs/horvath/MTOM/).

Contact: shorvath{at}mednet.ucla.edu

Supplementary information: Supplementary material is available at Bioinformatics online.

Associate Editor: Golan Yona

Received on August 27, 2006; revised on November 6, 2006; accepted on November 14, 2006

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