Table 2: Expression databases and resources that can be used to prioritize candidate genes.
Individual specialty resources such as ABA, GENSAT and GUDMAP provide specialized data and resources to their respective communities. Broader resources looking at embryonic development include Eurexpress and GenePaint. The data from both these resources feeds into the larger EMAP project and the MGI-GXD. The development of the MGEIR database, which is a collaboration between the EMAP and GXD projects, will provide a centralized hub for murine gene expression data.
| Expression databases | Stages/Tissue | Aim and Scope of the Database | URL |
|---|---|---|---|
| ABA (Allen Brain Atlas) |
Embryonic to adult brain and spinal cord |
Database of gene expression patterns in the mouse brain and spinal cord. |
http://brain-map.org/ For mouse: http://mouse.brain-map.org/ |
| GENSAT (Gene Expression Nervous System Atlas) |
- 10.5/15.5 dpc heads - P7, adult brain |
Map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. The EGFP BAC-transgenic mice created by this project are available to the scientific community (278 new Cre driver lines). |
http://www.gensat.org/ |
| GUDMAP (GenitoUrinary Development Molecular Anatomy Project) |
- 14.5 dpc whole embryos |
Consortium of laboratories working to provide the scientific and medical community with tools to facilitate research into the GU system. |
http://www.gudmap.org/ |
| FaceBase | - various mouse, human and zebrafish |
Consortium generating data in support of advancing research into craniofacial development and malformation. Comprehensive Includes data from high-throughput genetic, molecular, biological, imaging and computational techniques. |
https://www.facebase.org |
| Eurexpress | - 14.5 dpc whole embryos |
A transcriptome atlas database for mouse embryo. | http://www.eurexpress.org/ee/ |
| GenePaint | - 10.5/14.5 dpc whole embryos - 15.5, P7, adult (P57) brain |
Digital atlas of gene expression profiles in the mouse. | http://www.genepaint.org/ |
| The e-Mouse Atlas Project (EMAP) which includes: EMA (The e-Mouse Atlas) EMAGE (Edinburgh Mouse Atlas of Gene Expression) eHistology (Online Atlas of Mouse Development) |
- 1 cell – 18.5 dpc embryo - P0-P57 |
EMA, the e-Mouse Atlas. A 3-D anatomical atlas of mouse embryo development including detailed histology. EMAGE, the e-Mouse Atlas of Gene Expression. Anatomy is reconstructed from serial sections of single embryos at each representative developmental stage enabling 3D graphical display and analysis of in situ expression data eHistology resource, allows interactive exploration of cellular- resolution color images detailing mouse development with annotations from the Kaufman “Atlas of Mouse Development”. |
EMA: http://www.emouseatlas.org/emap/ema/ EMAGE: http://www.emouseatlas.org/emage/ eHistology: http://www.emouseatlas.org/emap/eHistology/ |
| MGI-GXD (Mouse Genome Informatics Gene Expression Database) |
- 1 cell – 18.5 dpc embryo - adult |
GXD collects and integrates the gene expression information in MGI. Its primary emphasis is on endogenous gene expression during mouse development. It integrates different types of data and provides links to other resources to place the data into the larger biological and analytical context. |
http://www.informatics.jax.org/expression.shtml |
| MGEIR (Mouse Gene Expression Information Resource) |
Pulls data from GXD and EMAP |
MGEIR is a collaboration between the GXD project and the EMAP project. | Under development |
| 3D Atlas of Human Embryo Development |
Morphological data from Carnegie Stage 7–23 |
This resource is a morphological (not an expression) atlas. It has 3D fully reconstructed human embryos covering the phase of organogenesis, between Carnegie stage 7 (15–17 days old embryo) and 23 (56–60 days). |
http://www.3dembryoatlas.com/ |