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:
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analysis and classification of regulatory
and coding regions in diverse homeobox and related genes;
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describing mutations and knock-outs
of hox-genes, as well as hereditary diseases related to these genes;
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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);
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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;
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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:
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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);
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3D model of epithelial layer with a cell-level resolution
for representation of patterns of a gene-expression in imaginal
disks of Drosophila embryo;
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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
Copyright © 1994-2000 HOX-ProTeam