dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data

Scientific Reports
Vân Anh Huynh-Thu, Pierre Geurts

Abstract

The elucidation of gene regulatory networks is one of the major challenges of systems biology. Measurements about genes that are exploited by network inference methods are typically available either in the form of steady-state expression vectors or time series expression data. In our previous work, we proposed the GENIE3 method that exploits variable importance scores derived from Random forests to identify the regulators of each target gene. This method provided state-of-the-art performance on several benchmark datasets, but it could however not specifically be applied to time series expression data. We propose here an adaptation of the GENIE3 method, called dynamical GENIE3 (dynGENIE3), for handling both time series and steady-state expression data. The proposed method is evaluated extensively on the artificial DREAM4 benchmarks and on three real time series expression datasets. Although dynGENIE3 does not systematically yield the best performance on each and every network, it is competitive with diverse methods from the literature, while preserving the main advantages of GENIE3 in terms of scalability.

References

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Citations

Jul 11, 2019·Journal of Bioinformatics and Computational Biology·Jamshid PirgaziMaryam Jalilkhani
Jul 12, 2019·Journal of Bioinformatics and Computational Biology·Shuhei KimuraMariko Okada
May 21, 2019·PLoS Genetics·Michael R WarnerTimothy A Linksvayer
Apr 24, 2020·Scientific Reports·Jacopo CirroneDennis E Shasha
Aug 28, 2020·Frontiers in Immunology·Bhavjinder K DhillonRobert E W Hancock
Aug 5, 2020·G3 : Genes - Genomes - Genetics·Sophie A HarringtonCristobal Uauy
Jan 30, 2021·PLoS Computational Biology·Jonathan LuBarbara E Engelhardt
Apr 18, 2020·Current Opinion in Biotechnology·Mun Su KwonHyun Uk Kim
Mar 7, 2021·Genes·Vera-Khlara S Oh, Robert W Li
Apr 21, 2021·Briefings in Bioinformatics·Ye Yuan, Ziv Bar-Joseph
Mar 5, 2021·Journal of Bioinformatics and Computational Biology·Jamshid PirgaziAlireza Khanteymoori
May 3, 2021·The EMBO Journal·Nathalia AlmeidaFrancesca M Spagnoli
Mar 6, 2021·Annual Review of Plant Biology·Jose M AlvarezGloria M Coruzzi
Jul 13, 2021·Bioinformatics·Julien MartinelliAnnabelle Ballesta

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Methods Mentioned

BETA
RNA-seq
gene knockdowns

Software Mentioned

CSI
TSNI
MCZ
Boost
Inferelator
GENIE3
MATLAB
Inferelator pipeline
R
VBSSM

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