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Network propagation to identify sub-networks associated with the phenotype.

Network propagation algorithm aids in inferring the altered sub-networks or signaling pathways in the given condition. The algorithm was originally developed by  Vanunu et al, 2010. We have noticed that standard network propagation suffered from gene-specific biases created by the connections in the network ('topology bias'). For example, genes with many neighbors will generally tend to accumulate higher scores independent of the gene expression data. Therefore, we devised an improved network propagation method that corrects for this topology bias.

R-package: BioNetSmooth1.0.0

Related Publications

Vanunu et al. A propagation based algorithm for inferring gene-disease associations. Proceedings of the German Conference on Bioinformatics 2008. German Conference on Bioinformatics. pp. 54–62.

Vanunu et al. Associating Genes and Protein Complexes with Disease via Network Propagation. PLoS Comput Biol 2010, 6(1):e1000641.

Hofree et al. Network-based stratification of tumor mutations. Nature Methods 2013, 10,1108–1115.