Protocol abstract
Nature Protocols 1, - 2551 - 2554 (2006)
Published online: 29 December 2006 | doi:10.1038/nprot.2006.300
Subject Categories: Computational and theoretical biology | Genetic analysis | Genomics and proteomics
The mode-of-action by network identification (MNI) algorithm: a network biology approach for molecular target identification
Heming Xing1,2 & Timothy S Gardner1
Abstract
This protocol details the use of the mode-of-action by network identification (MNI) algorithm to identify the gene targets of a drug treatment based on gene-expression data. Investigators might also use the MNI algorithm to identify the gene mediators of a disease or the physiological state of cells and tissues. The MNI algorithm uses a training data set of hundreds of expression profiles to construct a statistical model of gene-regulatory networks in a cell or tissue. The model describes combinatorial influences of genes on one another. The algorithm then uses the model to filter the expression profile of a particular experimental treatment and thereby distinguish the molecular targets or mediators of the treatment response from hundreds of additional genes that also exhibit expression changes. It takes 
1 h per run, although run time is significantly affected by the size of the genome and data set.
- Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA.
- Cellicon Biotechnologies, Inc., 222 Berkeley Street, Suite 1040, Boston, Massachusetts, 02116, USA.
Correspondence to: Timothy S Gardner1 e-mail: tgardner@bu.edu
