Table 3 Summary of gene expression atlases and databases surveyed

Expression patterns for C. elegans promoter::GFP fusions

Database of expression patterns of transgenic animals with promoter::GFP fusions

body

embryo through adult

http://gfpweb.aecom.yu.edu/index

A project of the British Columbia C. elegans Gene Expression Consortium

[69]

WormBase (“WormMine” tool)

Community repository of molecular and genetic data from the literature, submissions, and collaborating projects

body

embryo through adult

http://www.wormbase.org

An international consortium of researchers, based at Caltech (Pasadena, CA, USA)

[70]

[46]

GEISHA

Community repository of in situ hybridization data acquired from high-throughput screens and the literature

body

egg through first six days of development

http://geisha.arizona.edu/geisha

Gallus Expression in Situ Hybridization Analysis

Hosted by Parker Antin’s group at the University of Arizona (Tuscaon, AZ, USA)

[71]

[72]

[73]

ANISEED (“Gene Expression & Function” section)

Community repository of expression data from the literature, submissions, and collaborating projects

body

egg through adult

http://www.aniseed.cnrs.fr

Ascidian Network for In Situ and Embryological Data

A collaboration among ascidian researchers led by Patrick Lemaire at the CRM (Montpellier, France)

[47]

[48]

BDGP expression patterns

Database of in situ hybridization patterns

body

all embryonic stages

http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl

Berkeley Drosophila Genome Project

From the laboratory of Susan Celniker at the Lawrence Berkeley Laboratory (Berkeley, CA, USA)

[74]

[75]

[76]

FlyBase (“QuickSearch” tool)

Community repository of molecular and genetic data from the literature and direct submissions

body

egg through adult

http://flybase.org

From an international consortium of Drosophila researchers

[77]

[78]

[79]

FlyExpress

A tool for searching expression patterns using images data from BDGP and Fly-FISH

body

all embryonic stages

http://www.flyexpress.net

From the laboratory of Sudhir Kumar at Arizona State University (Tempe, AZ, USA)

[40]

[80]

Fly-FISH

Database of in situ hybridization patterns

body

early embryonic stages and third instar larva

http://fly-fish.ccbr.utoronto.ca

From the laboratory of Henry Krause at the University of Toronto (Toronto, Ontario, Canada)

[81]

MEPD

Database of expression patterns for genes (in situ hybridization) and regulatory sequences (fluorescent reporters)

body

egg through adult

http://mepd.cos.uni-heidelberg.de/mepd

Medaka Expression Pattern Database

A project within the Medaka Genome Initiative, from the laboratory of Joachin Wittbrody at University of Heidelberg Heidelberg, Germany)

[82]

[83]

[84]

Allen Developing Mouse Brain Atlas (“AGEA” section)

Atlas of spatially correlated expression patterns derived from in situ hybridizations on histological sections

brain

four embryonic stages (E11.5, 13.5, 15.5, 18.5), four post-natal stages (P4, 14, 28)

http://developingmouse.brain-map.org/agea/show

Anatomic Gene Expression Atlas of the Allen Developing Mouse Brain Atlas

Produced by the Allen Institute for Brain Sciences (Seattle, WA, USA)

[85]

[86]

[87]

[36]

EMBRYS

Database of in situ hybridization patterns, using whole mounts

body

three embryonic stages (E9.5, 10.5, 11.5)

http://embrys.jp/embrys/html/MainMenu.html

Note: no longer available online

From the laboratory of Hiroshi Asahara at the Systems BioMedicine Laboratory of the National Research Institute for Child Health and Development (Tokyo, Japan)

[88]

[89]

EMAGE

Community repository of molecular and genetic data from the literature and direct submissions

body

all post-implantation stages

http://www.emouseatlas.org/emage/home.php

e-Mouse Atlas of Gene Expression

Led by Duncan Davidson and Richard Baldock within the Medical Research Council Human Genetics Unit at the University of Edinburgh (Edinburgh, Scotland)

[56]

[90]

[91]

[58]

[92]

[93]

Eurexpress

Database of in situ hybridization patterns, using histoloogical sections

body

one embryonic stage (E14.5)

http://www.eurexpress.org/ee

From a consortium of European researchers

[94]

GXD

Community repository of expression data from the literature, direct submissions, and collaborating projects

body

all embryonic stages, postnatal

http://www.informatics.jax.org/gxd

Mouse Gene Expression Database

A Mouse Genome Informatics resource from Jackson Laboratory (Bar Harbor, ME, USA)

[95]

[96]

[97]

[98]

GENSAT

Database of in situ hybridization patterns and data from transgenic mice with EGFP reporter genes

nervous system

one embryonic stage (E15.5), postnatal (P7), adult

http://www.gensat.org/index.html

Gene Expression Nervous System Atlas

From the laboratory of Nathaniel Heinz at The Rockefeller University (New York, NY, USA)

[99]

[100]

GenePaint

Database of in situ hybridization patterns, using histological sections

body

three embryonic stages (E10.5, 14.5, 15.5), postnatal (P7), adult

http://genepaint.org

Led by Gregor Eichele at the Max Planck Institute of Biophysical Chemistry (Göttingen, Germany)

[101]

GUDMAP

Community repository of expression data from the GUDMAP consortium

urogenital system

mid-embryonic development through adult

http://www.gudmap.org

GenitoUrinary Molecular Anatomy Project

From an international consortium of researchers

[102]

[103]

[104]

Xenbase

Community repository of expression data from the literature, submissions, and collaborating projects

body

all stages through adult

http://www.xenbase.org

Led by Peter Vize at the University of Calgary (Calgary, Canada)

[105]

[106]

XenMARK expression patterns

Database of in situ hybridization patterns, using whole mounts

body

32-cell stage through tadpole

http://genomics.crick.ac.uk/apps/XenMARK

From the laboratory of Michael Gilchrist at the MRC National Institute for Medical Research (London, UK)

[38]

GEMS

Database of in situ hybridization patterns

body

gastrula through hatching

http://bio-imaging.liacs.nl/liacsgems.html

Note: no longer available online

Gene Expression Management System

Produced by the Imagery & Media Group at Leiden University (Leiden, Netherlands)

[107]

ZFIN

Community repository of molecular and genetic data from literature and direct submissions

body

zygote through adult

http://zfin.org

Zebrafish Model Organism Database (also known as the Zebrafish Information Network)

Based at the University of Oregon (Eugene, OR, USA)

[108]

[109]

[110]