HOX Pro database

SPIROV SPIROV at iephb.nw.ru
Tue Dec 12 05:50:11 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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