Gene networks

Description of function and network algorithms used for gene network visualization... 

Ekins S, Giroux CN, Nikolsky Y, Bugrim A, Nikolskaya T. A signature gene network approach to toxicity. Toxicologist 2005 84. 

Gene network identification Identify prevalent expression patterns (gene clusters) and then identify DNA sequence patterns This approach has been used to find regulatory elements in yeast. It will soon be used to discover coregulated genes in other organisms (including humans). 

Rosenfeld, J.M., Vargas, R., Jr, Xie, W. and Evans, R.M. (2003) Genetic profiling defines the xenobiotic gene network controlled by the nuclear receptor pregnane X receptor. Molecular Endocrinology, 17, 1268-1282. 

Control of gene expression is also clearly different in the two species and this is likely to be of profound importance. Scientists have looked at which of 4000 genes in brain are turned on at the same time, a measure of connections in gene networks. Clear differences have been revealed. For example, in the cerebral cortex, 17-18% of the revealed gene network connections are unique to humans. 

Obayashi, T., Hayashi, S., Shibaoka, M., Saeki, M., Ohta, H. and Kinoshita, K. (2008) COX-PRESdb A Database of Coexpressed Gene Networks in Mammals. Nucleic Acids Res, 36, D77-82. 

Paulsson, J. Summing up the noise in gene networks. Nature 2004, 427 415 418. 

A. Becskei and L. Serrano. Engineering stability in gene networks by autoregulation. Nature, 405 590-593,2000. 

Retinoid acids (RAs), the active retinoid derivatives of vitamin A, regulate complex gene networks. The pleiotropic effects of active retinoids are transduced by their cognate nuclear receptors, retinoid X receptors (RXRs) and retinoic add receptors... 

---