PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data.

Bioinformatics
Gourab Ghosh RoyShan He

Abstract

Inferring gene regulatory networks (GRNs) from expression data is a significant systems biology problem. A useful inference algorithm should not only unveil the global structure of the regulatory mechanisms but also the details of regulatory interactions such as edge direction (from regulator to target) and sign (activation/inhibition). Many popular GRN inference algorithms cannot infer edge signs, and those that can infer signed GRNs cannot simultaneously infer edge directions or network cycles. To address these limitations of existing algorithms, we propose Polynomial Lasso Bagging (PoLoBag) for signed GRN inference with both edge directions and network cycles. PoLoBag is an ensemble regression algorithm in a bagging framework where Lasso weights estimated on bootstrap samples are averaged. These bootstrap samples incorporate polynomial features to capture higher-order interactions. Results demonstrate that PoLoBag is consistently more accurate for signed inference than state-of-the-art algorithms on simulated and real-world expression datasets. Algorithm and data are freely available at https://github.com/gourabghoshroy/PoLoBag. Supplementary data are available at Bioinformatics online.

References

May 19, 2007·Nature Reviews. Genetics·Uri Alon
May 8, 2008·BMC Bioinformatics·Philippe VeberAnne Siegel
Feb 3, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Daniel MarbachDario Floreano
Apr 8, 2009·Annals of the New York Academy of Sciences·Mika GustafssonJesper Tegnér
Jun 10, 2009·Briefings in Bioinformatics·Wei-Po Lee, Wen-Shyong Tzou
Feb 27, 2010·PloS One·Robert J PrillGustavo Stolovitzky
Apr 27, 2010·Physics of Life Reviews·Timothy S Gardner, Jeremiah J Faith
Sep 24, 2010·PloS One·Robert KüffnerRalf Zimmer
Oct 12, 2010·PloS One·Vân Anh Huynh-ThuPierre Geurts
Dec 18, 2010·Nature Reviews. Genetics·Albert-László BarabásiJoseph Loscalzo
Mar 1, 2011·The Annals of Applied Statistics·Sijian WangJi Zhu
Jul 15, 2015·Algorithms for Molecular Biology : AMB·Pegah KhosraviGary D Bader
Sep 1, 2018·Bioinformatics·Daniel MorganErik L L Sonnhammer
Oct 28, 2019·Molecular Biology and Evolution·Amitesh AnandBernhard O Palsson

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