dorsal/arxiv
View SchemaModeling Genetic Networks from Clonal Analysis
| Authors | Radhakrishnan Nagarajan, Jane E. Aubin, Charlotte A. Peterson |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0412047 |
| URL | https://arxiv.org/abs/q-bio/0412047 |
| DOI | 10.1016/j.jtbi.2004.05.008 |
| Journal | J Theor Biol. 2004 Oct 7;230(3):359-73 |
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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"abstract": "In this report a systematic approach is used to determine the approximate\ngenetic network and robust dependencies underlying differentiation. The data\nconsidered is in the form of a binary matrix and represent the expression of\nthe nine genes across the ninety-nine colonies. The report is divided into two\nparts: the first part identifies significant pair-wise dependencies from the\ngiven binary matrix using linear correlation and mutual information. A new\nmethod is proposed to determine statistically significant dependencies\nestimated using the mutual information measure. In the second, a Bayesian\napproach is used to obtain an approximate description (equivalence class) of\nnetwork structures. The robustness of linear correlation, mutual information\nand the equivalence class of networks is investigated with perturbation and\ndecreasing colony number. Perturbation of the data was achieved by generating\nbootstrap realizations. The results are refined with biological knowledge. It\nwas found that certain dependencies in the network are immune to perturbation\nand decreasing colony number and may represent robust features, inherent in the\ndifferentiation program of osteoblast progenitor cells. The methods to be\ndiscussed are generic in nature and not restricted to the experimental paradigm\naddressed in this study.",
"arxiv_id": "q-bio/0412047",
"authors": [
"Radhakrishnan Nagarajan",
"Jane E. Aubin",
"Charlotte A. Peterson"
],
"categories": [
"q-bio.MN",
"q-bio.GN"
],
"doi": "10.1016/j.jtbi.2004.05.008",
"journal_ref": "J Theor Biol. 2004 Oct 7;230(3):359-73",
"title": "Modeling Genetic Networks from Clonal Analysis",
"url": "https://arxiv.org/abs/q-bio/0412047"
},
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