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

Submitted: 28 May 2010
Accepted: 22 October 2010
Published: 25 November 2010
Abstract Views: 1943
PDF: 528
HTML: 1329
Supplementary data table: 0
Publisher's note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Authors

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.

Dimensions

Altmetric

PlumX Metrics

Downloads

Download data is not yet available.

Citations

Supporting Agencies

National Institute of Advanced Industrial Science and Technology
Sachiyo Aburatani, Computational Biology Research Center, AIST
Research Scientist, Cell Function Design Team, Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)

How to Cite

Aburatani, S. (2010). Development of network inference among LexA/ RecA-dependent manner genes in the SOS response. Journal of Nucleic Acids Investigation, 1(1), e13. https://doi.org/10.4081/jnai.2010.1871