A posterior probability approach for gene regulatory network inference in genetic perturbation data
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Publication:326558
DOI10.3934/MBE.2016041zbMATH Open1388.62338arXiv1603.04835OpenAlexW2302531807WikidataQ31138678 ScholiaQ31138678MaRDI QIDQ326558FDOQ326558
Authors: William Chad Young, Ka Yee Yeung, 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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Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Systems biology, networks (92C42)
Cites Work
- Bayesian model averaging: A tutorial. (with comments and a rejoinder).
- Title not available (Why is that?)
- Title not available (Why is that?)
- Sharp Thresholds for High-Dimensional and Noisy Sparsity Recovery Using $\ell _{1}$-Constrained Quadratic Programming (Lasso)
- Model uncertainty
- Title not available (Why is that?)
- Bayesian Model Averaging for Linear Regression Models
- Bayes Factors
- Autoregressive models for gene regulatory network inference: sparsity, stability and causality issues
- Significance analysis of microarrays applied to the ionizing radiation response
- Minimax risks for sparse regressions: ultra-high dimensional phenomenons
- Title not available (Why is that?)
Cited In (24)
- An empirical Bayesian method for estimating biological networks from temporal microarray data
- Gene regulatory networks. Methods and protocols
- Deep large-scale multi-task learning network for gene expression inference
- Bayesian inference of gene regulatory networks: From parameter estimation to experimental design
- Reverse engineering gene regulatory networks using approximate Bayesian computation
- Dynamic network reconstruction from heterogeneous datasets
- Mania: a gene network reverse algorithm for compounds mode-of-action and genes interactions inference
- Inferring gene networks from steady-state response to single-gene perturbations
- Inferring gene regulatory networks by an order independent algorithm using incomplete data sets
- Identifying dynamical time series model parameters from equilibrium samples, with application to gene regulatory networks
- Reciprocal graphical models for integrative gene regulatory network analysis
- Inferring gene regulatory networks by PCA-CMI using Hill climbing algorithm based on MIT score and SORDER method
- Inferring gene networks using robust statistical techniques
- A genetic regulatory network based method for multi-objective sequencing problem in mixed-model assembly lines
- Context-Specific Nested Effects Models
- Defining a robust biological prior from pathway analysis to drive network inference
- Identifying gene regulatory networks from experimental data
- WENDY: covariance dynamics based gene regulatory network inference
- Mechanistic gene networks inferred from single-cell data with an outlier-insensitive method
- Inference of gene regulatory networks using Bayesian nonparametric regression and topology information
- Second order optimization for the inference of gene regulatory pathways
- Large-scale local causal inference of gene regulatory relationships
- Learning a nonlinear dynamical system model of gene regulation: A perturbed steady-state approach
- Constrained community-based gene regulatory network inference
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