Databases and Systems

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In February 1998, a ‘cDNA and EST Expression’ search was added. Unlike the
MGD ‘Molecular Probes and Segments’ search, the GXD format enables better
searching on source data associated with expressed sequences. Particularly, tissue,
age, cell line, and library are prominent search fields.
In June 1998, the first large-scale expression data set was searchable through the
‘Gene Expression Data’ query form. These data, generated by T. Freeman (Sanger
Centre, U.K.) include RT-PCR assays for 517 genes in 45 mouse tissues from 6-8
week old animals and from 15 day old embryos. Assay data include primary data on
each sample prepared, expression profiles for each sample in each experimental gel,
and images of the gels.
Importantly, although only limited expression data are available at this writing,
GXD is poised to undergo rapid data expansion. The database is now implemented to
capture and make available other datasets and several other types of expression
information. Expression patterns are described by a comprehensive dictionary of
anatomical terms that has been developed in collaboration with Drs. Bard and
Kaufmann of the University of Edinburgh and Drs. Davidson and Baldock of the
MRC, Western General Hosptial, Edinburgh. Further, editorial interfaces for
capturing and updating assay data from publications and image scanning are in place.
Some expression data will be acquired from annotation of the literature by
database editors. However, because only a fraction of the gene expression data that a
laboratory generates actually appears in published form, it is anticipated that GXD
data largely will come from electronic data submissions. The Gene Expression
Annotator (GEA) has been developed for this purpose and is currently being tested
by several laboratories. The Annotator prototype provides important features for
capturing standardized descriptions of gene expression data, validating data, and
submitting data files. GEA supports a drag-and-drop facility for importation and
indexing of image files, a hierarchical look-up list for embryonic anatomy, and links
to resources such as MGD and GenBank for verifying nomenclature and describing
probes [ 18].
With the sum of these developments, GXD will quickly expand and new data sets
and features can be expected to appear regularly on the Mouse Genome Informatics
WWW site.
The Mouse Genome Informatics (MGI) WWW site
MGD and GXD together provide a unique resource for analyzing how the structural
genome, through developmental pathways, produces observed phenotypes (Figure 3).
These databases are tightly integrated to enable comprehensive analysis of genotype,
expression, and phenotype data. Further, as a practical consideration, because MGD
already contains many data types that need to be shared with GXD ( e.g., data on
genes, molecular probes, inbred and mutant strains, references), efficiency is gained
by coordinating maintenance of these data.