Table 4 Anatomical representations within the gene expression atlases and databases
Atlas or database | Types of graphicsa | Controlled vocabulary or ontology for anatomyb |
|---|---|---|
C. elegans | ||
Expression patterns for C. elegans promoter::GFP fusions | • fluorescence micrographs • confocal micrographs (as projections and volumes) • DIC micrographs with fluorescence overlays | project-specific vocabulary |
WormBase (“WormMine” tool) | • various types submitted • Virtual Worm model with regions of gene expression highlighted | C. elegans Gross Anatomy Vocabulary C. elegans Development Vocabulary |
Chicken | ||
GEISHA | • various types submitted | project-specific vocabulary |
Ciona intestinalis | ||
ANISEED (Expression Data section) | • various types submitted | Ciona Developmental Ontology |
Drosophila | ||
BDGP expression patterns | • brightfield micrographs (whole mounts, colorimetric assay) | Drosophila Anatomy Ontology |
FlyBase (“QuickSearch” tool) | – | Drosophila Anatomy Ontology |
FlyExpress | • graphics from BDGP and Fly-FISH | vocabularies from BDGP and Fly-FISH |
Fly-FISH | • confocal micrographs | project-specific vocabulary |
Medaka | ||
MEPD | • brightfield micrographs (whole mounts, colorimetric assay for gene expression) • fluorescence micrographs (for regulatory element expression) | MFO |
Mouse | ||
Allen Developing Mouse Brain Atlas (“AGEA” section) | • brightfield micrographs (histological sections, colorimetric assay) • standardized 3D brain models with regions of expression highlighted | Allen Developing Mouse Brain Atlas ontology |
EMBRYS | • brightfield micrographs (whole mounts, colorimetric assay) • AERO images (whole mounts, colorimetric assay) | project-specific vocabulary |
EMAGE | • various types submitted | EMAP anatomy ontology |
Eurexpress | • brightfield micrographs (histological sections, colorimetric assay) | EMAP anatomy ontology |
GXD | • various types submitted | EMAP anatomy ontology; MA |
GENSAT | • brightfield micrographs (histological sections, colorimetric assay) • confocal micrographs | project-specific vocabulary |
GenePaint | • brightfield micrographs (histological sections, colorimetric assay) | project-specific vocabulary |
GUDMAP | • various types submitted | EMAP anatomy ontology |
Xenopus | ||
Xenbase | • various types submitted | XAO |
XenMARK expression patterns | • brightfield micrographs (whole mounts, colorimetric assay) | project-specific vocabulary |
Zebrafish | ||
GEMS | • confocal micrographs | DAOZ |
ZFIN | • various types submitted | ZAO |