Modeling genetic networks from clonal analysis
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Publication:2186501
DOI10.1016/J.JTBI.2004.05.008zbMATH Open1447.92259arXivq-bio/0412047OpenAlexW1967885456WikidataQ80432328 ScholiaQ80432328MaRDI QIDQ2186501FDOQ2186501
Jane E. Aubin, R. Nagarajan, Charlotte A. Peterson
Publication date: 9 June 2020
Published in: Journal of Theoretical Biology (Search for Journal in Brave)
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.
Full work available at URL: https://arxiv.org/abs/q-bio/0412047
Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Systems biology, networks (92C42)
Cites Work
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