BLOBFISH: Bipartite Limited Subnetworks from Multiple Observations using Breadth-First Search with Constrained Hops

In analyzing gene regulatory network models, a common question is how members of a particular set of genes are connected. For example, one might want to explore network relationship between a set of differentially expressed genes, a gene set previously reported in the literature, or elements of one or more pathways. BLOBFISH uses a breadth-first search algorithm adapted to bipartite graphs to identify a compact subnetwork connecting the members of a pre-specified set of genes, providing a regulatory context that can shed light on specific mechanisms involved in a phenotype and its development. We demonstrate the use of BLOBFISH to extract gene regulatory subnetworks reflecting tissue specificity using publicly available data from the Genotype Tissue Expression (GTEx) project.