Inferring gene expression networks with hubs using a degree weighted Lasso approach

Bioinformatics
Nurgazy SulaimanovHeinz Koeppl

Abstract

Genome-scale gene networks contain regulatory genes called hubs that have many interaction partners. These genes usually play an essential role in gene regulation and cellular processes. Despite recent advancements in high-throughput technology, inferring gene networks with hub genes from high-dimensional data still remains a challenging problem. Novel statistical network inference methods are needed for efficient and accurate reconstruction of hub networks from high-dimensional data. To address this challenge we propose DW-Lasso, a degree weighted Lasso (least absolute shrinkage and selection operator) method which infers gene networks with hubs efficiently under the low sample size setting. Our network reconstruction approach is formulated as a two stage procedure: first, the degree of networks is estimated iteratively, and second, the gene regulatory network is reconstructed using degree information. A useful property of the proposed method is that it naturally favors the accumulation of neighbors around hub genes and thereby helps in accurate modeling of the high-throughput data under the assumption that the underlying network exhibits hub structure. In a simulation study, we demonstrate good predictive performance of the p...Continue Reading

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Citations

Apr 18, 2020·Current Opinion in Biotechnology·Mun Su KwonHyun Uk Kim
Jun 3, 2021·Biomolecules·Moon SajidParwinder Kaur
Nov 13, 2021·PloS One·Tyler Grimes, Somnath Datta

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