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bioRxiv · 10.1101/2025.03.11.642378

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

Eicher, T. D.·Ben Guebila, M.·Quackenbush, J.
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Abstract

SummaryIn 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.

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Eicher, T. D., Ben Guebila, M., Quackenbush, J.. 2025-03-13. BLOBFISH: Bipartite Limited Subnetworks from Multiple Observations using Breadth-First Search with Constrained Hops. https://doi.org/10.1101/2025.03.11.642378

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