GenExpress: an intellectual system for analysis of genomic regulatory sequences of humans and higher eukaryotes
N.A. Kolchanov, M.P. Ponomarenko, A.E. Kel, Yu.V. Ponomarenko, F.A. Kolpakov, A.S. Frolov, V.V. Soloviev*, A.G. Romashchenko, E.A. Ananko, E.V. Ignatieva, O.A. Podkolodnaya, I.L. Stepanenko, O.V. Kel, T.I. Merkulova, T.N. Goryachkovskaya, A.V. Kochetov, N.L. Podkolodny, G.B. Kolesov, S.V. Lavryushov, L.L. Kisselev**
Institute of Cytology and Genetics, , Novosibirsk, 630090, Russia;
*The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambs, CB 10 1S, UK
**Engelhardt Institute of Molecular Biology, 32 Vavilov Street, 117984 Moscow.
The intellectual system GenExpress designed for analysis of genomic regulatory sequences of higher eukaryotes comprises the following major units:
(1) the database of transcription regulatory regions of eukaryotic genes TRRD that contains the description of regulatory regions of 427 eukaryotic genes, including 2133 transcription factor binding sites, 78 composite regulatory elements, 593 enhancers, and other types of transcription-regulating elements;
(2) the database Activity that comprises the available data on the activity of the sites involved in the regulation of gene expression as well as the physico-chemical, conformational, and statistical DNA/RNA properties significant for the activity of these sites;
(3) the database for gene networks GeneNet that contains the information on groups of the genes functioning coordinately to provide expression of genetic information;
(4) a set of programs for detecting functional sites and predicting their activity;
(5) programs for visualization of the information contained in the listed databases and the results of analysis;
(6) semantic means to provide userís navigation in the system.
SRS (Sequence Retrieval System) query language was chosen for the system GenExpress, as it is widespread and Internet-compatible. GenExpress is available at /mgs/systems/geneexpress/. Applications of the system to analysis of the structure-function organization of human genomic nucleotide sequences are considered.
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