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Nat Protoc. 2006;1(6):2551-4.

The mode-of-action by network identification (MNI) algorithm: a network biology approach for molecular target identification.

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  • 1Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA.


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 approximately 1 h per run, although run time is significantly affected by the size of the genome and data set.

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