Large-scale local causal inference of gene regulatory relationships
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Publication:2302806
DOI10.1016/J.IJAR.2019.08.012zbMATH Open1470.92114arXiv1909.03818OpenAlexW2971808129WikidataQ130544869 ScholiaQ130544869MaRDI QIDQ2302806FDOQ2302806
Authors: Ioan Gabriel Bucur, Tom Claassen, Tom Heskes 
Publication date: 26 February 2020
Published in: International Journal of Approximate Reasoning (Search for Journal in Brave)
Abstract: Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput genetic data. Many of these computational methods are designed to infer individual regulatory relationships among genes from data on gene expression. We propose a novel efficient Bayesian method for discovering local causal relationships among triplets of (normally distributed) variables. In our approach, we score covariance structures for each triplet in one go and incorporate available background knowledge in the form of priors to derive posterior probabilities over local causal structures. Our method is flexible in the sense that it allows for different types of causal structures and assumptions. We apply our approach to the task of learning causal regulatory relationships among genes. We show that the proposed algorithm produces stable and conservative posterior probability estimates over local causal structures that can be used to derive an honest ranking of the most meaningful regulatory relationships. We demonstrate the stability and efficacy of our method both on simulated data and on real-world data from an experiment on yeast.
Full work available at URL: https://arxiv.org/abs/1909.03818
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Cited In (11)
- Minreg: A scalable algorithm for learning parsimonious regulatory networks in yeast and mammals
- Deep large-scale multi-task learning network for gene expression inference
- Gene pathways discovery in asbestos-related diseases using local causal discovery algorithm
- Deduction of a gene regulatory relationship framework from gene expression data by the application of graphical Gaussian modeling
- Inferring Regulatory Networks from Time Series Expression Data and Relational Data Via Inductive Logic Programming
- Identifying local co-regulation relationships in gene expression data
- Exploring gene causal interactions using an enhanced constraint-based method
- Inferring gene regulatory networks by PCA-CMI using Hill climbing algorithm based on MIT score and SORDER method
- A posterior probability approach for gene regulatory network inference in genetic perturbation data
- Efficient and scalable Bayesian statistical method for identifying causal relationships from intervention studies
- Large-Scale Hypothesis Testing for Causal Mediation Effects with Applications in Genome-wide Epigenetic Studies
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