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Development of network inference among LexA/ RecA-dependent manner genes in the SOS response

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Author(s): Sachiyo Aburatani

Journal: Journal of Nucleic Acids Investigation
ISSN 2036-7996

Volume: 1;
Issue: 1;
Start page: e13;
Date: 2010;
Original page

Keywords: Bioinormatics | Network Inferece | Microarray analysis

ABSTRACT
The expression of many genes varies under different conditions. The relationships among genes can be identified from DNA microarray data. To better understand the SOS response, I developed a network model of whole LexA/RecA-dependent manner genes in two genotypes of Escherichia coli from expression data after ultraviolet (UV) irradiation. First, all LexA/RecA-dependent manner genes were estimated by a combination of the Mann-Whitney U test and hierarchical clustering. Second, the relationships between genes were inferred from a graphical Gaussian model (GGM) combined with hierarchical clustering. Here, I incorporate a step-by-step procedure of the method developed in my previous study to identify interactions within larger clusters. The analysis suggested the presence of a sequential relationship between LexA/RecA-dependent manner gene groups in which the association between neighboring groups was positive while that between non-neighboring groups was negative. I suggest the inferred network provides information on the functional role of poorly defined genes whose expression patterns change according to LexA/RecA. Although relationships in the network require biological validation, the model presented here provides insights into potential LexA/RecA regulation following UV irradiation.
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