A posterior probability approach for gene regulatory network inference in genetic perturbation data

DOI10.3934/MBE.2016041zbMATH Open1388.62338arXiv1603.04835OpenAlexW2302531807WikidataQ31138678 ScholiaQ31138678MaRDI QIDQ326558FDOQ326558

Ka Yee Yeung, William Chad Young, Adrian E. Raftery

Publication date: 12 October 2016

Published in: Mathematical Biosciences and Engineering (Search for Journal in Brave)

Abstract: Inferring gene regulatory networks is an important problem in systems biology. However, these networks can be hard to infer from experimental data because of the inherent variability in biological data as well as the large number of genes involved. We propose a fast, simple method for inferring regulatory relationships between genes from knockdown experiments in the NIH LINCS dataset by calculating posterior probabilities, incorporating prior information. We show that the method is able to find previously identified edges from TRANSFAC and JASPAR and discuss the merits and limitations of this approach.

Full work available at URL: https://arxiv.org/abs/1603.04835

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zbMATH Keywords

Bayesian analysisstatisticsgene regulatory networkstatistical computation

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Systems biology, networks (92C42)

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Cited In (5)

• Mania: a gene network reverse algorithm for compounds mode-of-action and genes interactions inference
• Identifying dynamical time series model parameters from equilibrium samples, with application to gene regulatory networks
• A genetic regulatory network based method for multi-objective sequencing problem in mixed-model assembly lines
• Context-Specific Nested Effects Models
• Identifying gene regulatory networks from experimental data

Uses Software

• bnlearn
• minet
• Enrichr
• TRANSWESD
• ARACNE
• TRANSFAC
• JASPAR
• CGBayesNets

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