Inference on the structure of gene regulatory networks

DOI10.1016/J.JTBI.2022.111055zbMATH Open1483.92070arXiv2107.13099OpenAlexW4211005300MaRDI QIDQ2116003FDOQ2116003

Yanyan Li

Publication date: 15 March 2022

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: In this paper, we conduct theoretical analyses on inferring the structure of gene regulatory networks. Depending on the experimental method and data type, the inference problem is classified into 20 different scenarios. For each scenario, we discuss the problem that with enough data, under what assumptions, what can be inferred about the structure. For scenarios that have been covered in the literature, we provide a brief review. For scenarios that have not been covered in literature, if the structure can be inferred, we propose new mathematical inference methods and evaluate them on simulated data. Otherwise, we prove that the structure cannot be inferred.

Full work available at URL: https://arxiv.org/abs/2107.13099

zbMATH Keywords

differential equationindependenceinferencegene regulatory network

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

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Cited In (11)

• Title not available (Why is that?)
• Structure-function relations are subtle in genetic regulatory networks
• Computational Methods for Inference of Gene Regulatory Networks from Gene Expression Data
• A graphical chain model for inferring regulatory system networks from gene expression profiles
• Modeling Parsimonious Putative Regulatory Networks: Complexity and Heuristic Approach
• Inference on autoregulation in gene expression with variance-to-mean ratio
• Order-of-mutation effects on cancer progression: models for myeloproliferative neoplasm
• Inferring stable genetic networks from steady-state data
• Identifying gene regulatory networks from experimental data
• WENDY: covariance dynamics based gene regulatory network inference
• EVIDENCE OF SCALE-FREE TOPOLOGY IN GENE REGULATORY NETWORK OF HUMAN TISSUES

Uses Software

• ConGRI

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