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What is AREX?
Welcome to AREX, The ARabidopsis gene EXpression Database. This database
collects Arabidopsis gene expression data from genome-wide (Affymetrix microarrays)
and gene-specific (in situs, promoter::reporter constructs etc.) sources
and provides integrative search tools.
Currently the database contains only root gene expression data
but has the capability to contain data from any part of the plant.
Aims
(1) Integrate genome-wide and gene-specific ('traditional') types
of expression pattern data, using ontologies to describe data whenever
possible, in particular
to describe expression patterns.
(2) Provide user-friendly search tools, for example to search for genes
expressed with a certain pattern, or to search for the expression pattern
of specific genes (from gene-specific experiments and from microarray data).
Expression pattern predicted from the microarray data is called "digital in situ".
Data Content
Currently the database mostly contains root data produced by the Benfey Lab
from microarray experiments on sorted cells and promoter-GFP reporter experiments
(browse 'Publications'). It is our goal to also include similar public data produced
by other labs.
Root Data
The database was initially constructed to store root data, the organ on which
the Benfey lab
is working.
The Arabidopsis root increasingly is looked to as a valuable developmental
model system, resulting in a rapid accumulation of root genetic and molecular
data that needs to be organized in an efficient manner.
Moreover, we have developed a procedure whereby cells in
the root can be sorted by cell type using FACS and assayed for genome-wide
expression with microarrays, providing genome-wide cell-type specific
gene expression patterns.
Data Structure and Description
The database stores three types of data,
'experiments', 'genes', and 'publications'.
'Experiments' are either gene-specific (in situ, reporter, etc.) or genome-wide
(Affymetrix microarray).
Each 'experiment' has the following descriptive fields - those with an asterix
use ontologies whenever possible:
Privacy, Title, Gene(s), Authors, Date, Description, Related Publications,
Experiment_Type*, Organism*, Expression*, Growth Stage*, Data_Files.
More on Experiment_Type
For traditional experiments we list: (Type, Subtypes, Visualization, Imaging).
Type choices are (Transgenic, RNA in situ hybridization, Protein immunolocalization)
Subtype choices are (promoter fusion, protein fusion, enhancer trap, promoter trap, gene trap)
Visualization and imaging use this ontology: http://obo.sourceforge.net/cgi-bin/detail.cgi?image
For descriptions of microarray experiments, a standard needs to be developed
(probably based on MAGE-ML)
More on Organism
Use this ontology http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/.
Not implemented yet?
More on Expression
Expression patterns or cell-types used for microarray experiments are described using
the Plant Ontology (http://www.plantontology.org)
The 'genes' list already contains all the entries
of the Affymetrix full-genome chip annotation.
These entries may be updated or new entries may be added if necessary
when entering an experiment.
The 'publication' list contains the publications pertaining to the
experiments entered.
Note that you need to obtain permission from
the administrator to obtain write access.
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