Modeling genetic networks from clonal analysis

DOI10.1016/J.JTBI.2004.05.008MaRDI QIDQ2186501zbMATH OpenOpenAlexWikidataFDO

Authors R. Nagarajan, Jane E. Aubin, Charlotte A. Peterson

Publication date 9 June 2020

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

Full work available at URL https://arxiv.org/abs/q-bio/0412047

zbMATH Keywords

Bayesian networksmutual informationlinear correlationclonal analysisosteoblast differentiation

Mathematics Subject Classification ID

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

Abstract: In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine genes across the ninety-nine colonies. The report is divided into two parts: the first part identifies significant pair-wise dependencies from the given binary matrix using linear correlation and mutual information. A new method is proposed to determine statistically significant dependencies estimated using the mutual information measure. In the second, a Bayesian approach is used to obtain an approximate description (equivalence class) of network structures. The robustness of linear correlation, mutual information and the equivalence class of networks is investigated with perturbation and decreasing colony number. Perturbation of the data was achieved by generating bootstrap realizations. The results are refined with biological knowledge. It was found that certain dependencies in the network are immune to perturbation and decreasing colony number and may represent robust features, inherent in the differentiation program of osteoblast progenitor cells. The methods to be discussed are generic in nature and not restricted to the experimental paradigm addressed in this study.

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Cites work

• scientific article; zbMATH DE number 1303613 (Why is no real title available?)
• scientific article; zbMATH DE number 1493045 (Why is no real title available?)
• scientific article; zbMATH DE number 819507 (Why is no real title available?)
• scientific article; zbMATH DE number 1439344 (Why is no real title available?)
• scientific article; zbMATH DE number 3298430 (Why is no real title available?)
• A Bayesian method for the induction of probabilistic networks from data
• A Mathematical Theory of Communication
• Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. With a comment by J. A. Hartigan and a rejoinder by the authors
• Causation, prediction, and search. With additional material by David Heckerman, Christopher Meek, Gregory F. Cooper and Thomas Richardson.
• Equation of state calculations by fast computing machines
• Independent coordinates for strange attractors from mutual information.
• Monte Carlo sampling methods using Markov chains and their applications

Cited in

(1)

• Identifiability and inference of pathway motifs by epistasis analysis

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