Gene Networks

N.A. Kolchanov, E.A. Anan'ko, F.A. Kolpakov, O.A. Podkolodnaya, E.V. Ignat'eva, T.N. Goryachkovskaya, and I.L. Stepanenko

Gene network is a group of genes functioning in a coordinated manner to control vital processes in an organism. Each gene network includes several essential components:

• a group of genes which form a core of a gene network;
• proteins encoded by these genes;
• signal transduction pathways;
• negative and positive feedback which provide for autoregulation;
• low-molecular-weight compounds.

To accumulate the information on gene networks, a database GeneNet has been developed. At present, GeneNet contains the data on 16 gene networks which are arranged in six sections according to the subject concerned: lipid metabolism, steroidogenesis, erythropoiesis, antiviral response, plant seed development, and heat shock. Analysis of the data accumulated in GeneNet revealed the following principles of the gene network organization:

1. there is a great variety of molecular mechanisms which provide for a feedback regulation;
2. each gene network includes key genes which coordinate the function of other genes in the gene network;
3. one transcription factor activates many genes via a cassette mechanism;
4. gene networks are autoregulated via regulatory circuits with positive and negative feedback.

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Key words: genes, expression regulation, gene networks, databases, signal transduction pathways