GENEEXPRESS: A WWW-ORIENTED INTEGRATOR FOR THE DATABASES AND COMPUTER SYSTEMS FOR STUDYING THE EUKARYOTIC GENE EXPRESSION
Kolchanov N. A., Ponomarenko M. P., Kel A. E., Kondrakhin Y. V., Frolov A. S., Kolpakov F. A., Goryachkovskaya T. N., Kel O. V., Ananko E. A., Ignatieva E. V., Podkolodnaya O. A., Stepanenko I. L., Merkulova T. I., Babenko V. V., Vorobyie
Institute of Cytology & Genetics, 630090, Novosibirsk, Russia; FAX: +7(3832)356-558; E-mail: kol@bionet.nsc.ru ;; Institute of Computational Mathematics & Mathematical Geophysics, Novosibirsk, Russia; 2 Istituto Di Tecnologie Biomediche Avanzate,
The eukaryotic gene expression is one of the most complex biological
phenomena involving a number of molecular events. It may start by the cellular
reception of a definite stimulus which is, then, passed via the particular
signal transduction pathway to initiate transcription of the relevant genes.
Their pre-mRNAs are processed by 3'cutting/polyadenylation, capping, splicing,
and finally the corresponding proteins are translated from these mature
mRNAs. This totality of molecular events forms the particular gene network
that provides the cell response to the stimulus. The cellular and organismic
homeostases are maintained by their gene networks as well as cell/tissue
differentiation and development. Thus, investigation of the gene expression
is an integrative problem of biology. That is why we have developed GeneExpress
- the WWW-oriented integrator for the databases and computer systems for
studying the gene expression. The database GeneNet on molecular events
forming gene networks was assigned its integrative core. To study transcription,
this core was supplemented with the database TRRD on transcription regulatory
regions and the compilation TFBSC of the sequence sets of transcription
factor binding sites. The TRRD and TFBSC were linked to the computer system
RgScan recognizing the sites in DNA sequences. For translation, the database
on mRNA leaders was included and linked to the program predicting the High/Low
translation levels from a given mRNA sequence. The gene expression is also
quantitatively described by the system ACTIVITY compiling the functional
site activity magnitudes and linked with the programs predicting the activities
from site sequences. It is essential that the GeneExpress can and have
to progress and expand continuously to update and integrate new resources
for investigating other molecular events of the gene expression, such as
splicing, DNA/protein interactions, etc. To navigate GeneExpress, the SRS,
HTML, and Java viewers were developed (
http://wwwmgs.bionet.nsc.ru/systems/GeneExpress/).
The work was supported by grants of Russian Human Genome and Russian
Foundation for Basic Research.