Welcome to the MTOM Software Page:

Network Neighborhood Analysis and Module Detection

Ai Li (1) and Steve Horvath (1,2)
1 Dept. of Biostatistics, School of Public Health, UCLA
2 Dept. of Human Genetics, David Geffen School of Medicine, UCLA


Department of Human Genetics and Department of Biostatistics
University of California, Los Angeles, CA 90095


  1. Li A, Horvath S (2006) Network Neighborhood Analysis with the multi-node topological overlap measure. Bioinformatics. doi:10.1093/bioinformatics/btl581
  2. Li A, Horvath S. (2009) Network module detection: Affinity search technique with the multi-node topological overlap measure. BMC Res Notes. 2009 Jul 20;2:142.

Abstract for Neighborhood Analysis

A pair of nodes in a network is said to have high topological overlap if they are both strongly connected to the same group of nodes.
In gene networks, genes with high topological overlap have been found to have an increased chance of being part of the same biological pathway.

The use of topological overlap serves as a filter to exclude spurious or isolated connections. A topological overlap measure can be used in network analysis for finding similar nodes or for defining a neighborhood of an initial set of nodes.

The standard topological overlap measure allows one to measure pairwise topological overlap in an undirected network. Here we generalize this overlap measure to multiple nodes. The resulting multiTOM measure can be used to define a neighborhood of a initial set of nodes. We provide several applications which shows the use of these neighborhoods. The method is implemented in our MTOM software.



              Software MTOM

         Tutorial in Microsoft Word Format

         Update Record (2006-04-21)

Presentation Slides

              Link to talk: PowerPoint  PDF

Data Sets

          1. Fly Data Set

               Interaction Data Set

               Essential Genes

          2. Yeast Data Set (from MIPS)

               Interaction Data Set

               Cell Cycle Related Genes

          3. Yeast Data Set (from BioGrid)

               Interaction Data Set

               Essential Genes

          4. Brain Cancer Data Set

               Microarray Data Set

             Reference to this Data Set

Other material regarding weighted gene co-expression network analysis

             Weighted Gene Co-Expression Network Page



Please send your suggestions and comments to: shorvath@mednet.ucla.edu