HOX Pro database

SPIROV SPIROV at iephb.nw.ru
Mon Dec 11 14:44:18 EST 2000


                Dear Colleagues,
New release of the HOX Pro DB is available at: 
http://www.iephb.nw.ru/hoxpro 
The database is substantially updated and upgraded. 
Your feedback will be appreciated! 
We are looking for partners/collaborators both for future
developments of the DB and for future joint projects. 
        Yours sincerely, 
                        Alex Spirov
P.S. The US mirror at 
http://www.mssm.edu/molbio/hoxpro
will be updated in two weeks. 
-----------------------------------
  Alexander V. Spirov (PhD)
The Sechenov Institute of Evolutionary Physiology &
 Biochemistry, Thorez Pr. 44,
St.Petersburg, 194223, Russia
fax +7 (812)552 3012;  phone/fax + 7 (812)552 3219
http://www.iephb.nw.ru/~spirov
Email: spirov at iephb.nw.ru
---------------------------------
Homeobox Genes DataBase

HOX Pro DB: structural and functional genomics of hox
ensembles



    The database HOX Pro contains information about organization,
functions and evolution of gene ensembles, key roles in which play
homeobox-genes. It is now clear that the homeobox motif is well
conserved across metazoan phyla. It has been established experimentally
that a subset of genes containing this motif play key roles in the
orchestration of gene expression during development. Cross-regulatory
functional interactions join these genes-controllers into genetic
networks. It is the networks of genes that control patterning of an
embryo, morphogenesis, cell differentiation and involved in malignant
transformation.

Members of HOX-clusters are of particular importance in specifying the
overall animal body plan, and have been the objects of intensive study.
For these reasons, the homeobox containing genes are a natural choice
for the subject matter of a database concerned with gene function in
development at multiple levels.

    The HOX-Pro database is aimed at: 

      1.analysis and classification of regulatory and coding regions in
diverse homeobox and related genes;

      2.describing mutations and knock-outs of hox-genes, as well as
hereditary diseases related to these genes;

      3.graphical representation, comparisons and classification of
hox-genes expression patterns and profiles (sea urchin blastula,
Drosophila blastoderm and imaginal discs, vertebrate limbs, mammalian
brain, human EC cells);

      4.comparative analysis of organization of "hox-based" genetic
networks the nematode Caenorhabditis elegans  the sea urchins
Strongylocentrotus purpuratus and other echinids, the fruit flies
Drosophila melanogaster and D.virilis, the vertebrates chicken
and mouse;

      5.analysis of phylogeny and evolution of homeobox genes and
clusters. 

    The DB primary location is http://www.iephb.nw.ru/hoxpro
    
    The database is also mirrored at http://www.mssm.edu/molbio/hoxpro

    The HOX Pro contains a broad spectrum of information including
images, diagrams and animations. Currently this amounts to approximately
700 html-pages together with 400 images which contain information on 200
groups of genes and 90 promoters, in turn linked to maps of 15 HOX
clusters and 9 genetic networks. For today it is known about 700 sequences
of individual hox-genes of animals classified approximately in 200
homologous or paralogous groups.

    The HOX Pro database contains data on the structural and functional
organization of the transcriptional regulatory machinery of homeobox and
functionally related genes. The hierarchical organization of transcription
regulation of metazoan genes is incorporated into the database schema.
HOX Pro includes a hypertext description of the mechanisms of homeobox
gene activation as well as the functional characteristics of proteins
encoded by homeobox-containing and functionally related genes.

    Graphical representation of HOX clusters and Hox-based networks is
accomplished by means of flow and 3D diagrams, JavaScript diagrams, and
Java applets. In current version of the DB three classes of graphic 3D
models of gene-expression patterns are presented:

      1. Java applets for representation of detailed picture of gene
activity in ~3000 nuclei of Drosophila early embryo (blastoderm stage)
and for representation of patterns of a gene-expression of sea urchin
early embryo (cleavage stage, blastula and gastrula);

      2. 3D model of epithelial layer with a cell-level resolution for
representation of patterns of a gene-expression in imaginal
disks of Drosophila embryo;

      3. 3D model of organs and parts of vertebrate embryos (limb buds,
embryo eye, embryo brains) in standard 3D formats for representation
of patterns of a gene expression.

    The HOX Pro also contains links to other databases such as GeneBase,
FlyBase, TRANSFAC, COMPEL, EPD, EMBL, GeNet and The Interactive Fly. 

    The long-term goal of HOX Pro is the reconstruction and prediction
of functional genetic regulatory pathways from all relevant biological
assays. These include not only sequence data but also information about
protein binding, expression patterns, and so on. We hope to integrate
the molecular aspects of modern developmental biology by utilizing the
information pathways that run from sequence data to developing organs
and tissues.

Reference: Spirov A.V., Bowler T. and Reinitz J., (2000) HOX-Pro:
A Specialized Database for Clusters and Networks of Homeobox Genes,
NUCLEIC ACIDS RESEARCH, 28:337-340,
http://www3.oup.co.uk/nar/Volume_27/Issue_01/gkd054_gml.html
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