The main data is gene expression data acquired through whole mount in situ hybridisation. This data has been generated in-house as well as integrated from different public resources like BDGP, ZFIN, MGI and MEPD. The database schema is also capable of storing high resolution expression data from other experiments like antibody stainings and trangenics.

No. All data is public and searchable without login. Only data which is in the annotation pipeline is not accessible, but will be released, when annotation is complete. At the moment we do not have any remote annotation, so we have disabled the login field.

You can download the data you find in tables on our web page. However we can not provide a bulk download at the moment for all data as we re-distribute data from other sources.

You can search genes by identifiers and expression annotation with the search gene menu. (described in Help)

Go to search Gene by Expression (Text) and select bilateria. (described in Help)

For data submission you need an account. Please contact us. When logged in you will be able to access our annotation tool.

Yes. When developing the database schema we took care to be able to capture all fields required for MISFISHIE compliancy.

MISFISHIE stands for Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments. It can be used to develop an exchange format for high resolution gene expression data.

Mouse and medaka still use the cross product of stage and anatomy instead of an independant anatomy ontology. Others like zebrafish started with the same ontology structure, but have updated in the meantime.

We directly show images for medaka and drosophila only at the moment, because of copyright issues. However images of expression patterns of the other species are linked. You can access them easily by either following the expression pattern- or gene- links. We will work on getting permission to show more images within our pages.

The Bilateria are all animals having a bilateral symmetry, i.e. they have a front and and a back end, as well as an upside and downside. Radially symetrical animals like jellyfish have a topside and downside, but no front and back. The bilateralians are a major group of animals, including the majority of phyla.
Wikipedia: Bilateria
All species in 4DXpress belong to the group of Bilateria. If you select Bilateria in a menu, all species will be selected. Also the mapping developmental stages are common to all Bilaterians.

Wildcards (*, %, ?) are not supported. However it will be checked if the database fields contain the search term you have entered.

Releases are named by their major.minor.subminor version numbering scheme according to the following rules:
Starting with 4DXpress 1.x, the "1" indicates a major release of 4DXpress. This number is incremented at each public resources update (model organism databases as well as EnsEMBL).
For 4DXpress 1.1.x, the second number indicates the add of new features, while the last indicates a bug fix release.

The Jaccard distance has been calculated between the expression vectors of gene pairs. The expression binary vector was compiled considering stage and anatomy. If a gene is expressed (has positive annotation) at a given stage in a given anatomical structure the vector value is set to true, otherwise to false.
The Jaccard similarity coefficient is defined as the size of the intersection divided by the size of the union of the sample vectors:

Jaccard similarity coefficient:       J(A, B) = | A ∩ B | / | A ∪ B |

Jaccard distance:       J_δ(A, B) = 1 - J(A, B)

The distance value is supposed to estimate how different expression patterns are. However the calculation of this value depends on the extent and quality of the annotation. Thus, in the cases where annotations are incomplete or have been done inconsistently this measure might be misleading. Also, this method treats all anatomical structures equally. Relations defined in the anatomy ontology are not taken into account. Still, the Jaccard distance provides a quick and easy way for identifying similarly annotated genes.