Need Help

If you see the lightbulb symbol below you can get specific help for the interface you are using at the moment.

Search Gene

Genes can be searched either by a range of external identifiers, symbol, name or by their expression pattern annotation.

• by ID

  Genes can be searched by a range of full or partial external identifiers (eg. ensembl, zfin, flybase, mgi), symbols, gene names, gene description lines.
  examples:

  ensembl ids	ENSMUSG00000025219
  mouse mgi ids	MGI:96197
  gene names	homeobox, hox, pax, fgf, fibroblast growth,

  Fast and easy access to unique ids is provided by the ID-Finder in the page header (more details...).

• by Expression (Ontology)

  Selecting a species the corresponding stage and anatomy ontologies are loaded and information is provided on how many genes where annotated with this term.

• by Expression (Text)

  Either a single species can be secelcted; or when selecting "Bilateria" a cross species query can be done. A list of search terms can be entered manually and is guided by autocompletion of terms which have been used for annotation.

Gene List

Upon sending the query a gene list is returned, which provides the user with a summary overview of genes that match the query.

• To see the complete entry for each gene please click on the 4DXpress Link
• By default this list is ordered by orthologous group. COG ID
• The list can be ordered by clicking on one of the underlined column headers.
• Patterns : The number of gene expression patterns, which have been annotated for this gene
• Symbol : is the gene symbol with a species prefix to make it unique.
• When selecting a list of gene using the checkbox, you can either search for the orthologs of this list of genes or compare their expression patterns.

Gene View

When picking an individual gene entry the full information on that gene is displayed: external identifiers, gene description, expression pattern annotation using stage and anatomy ontologies, images of stained embryos, orthology relation ships (visualised as a network).

This information is subdivided:
• The Gene Details Panel describes the internal identifier, symbol, gene name and species. The external links provide links to the databases where you can find more information of that kind.
• The Expression Pattern Panel describes the gene expression pattern with images and annotation. The Pattern Links provide external links to the database, which provided the expression data. These are important links for the genes without images. Images can be access via these links. A list of genes is provided with similar gene expression patterns. Similarity is calculated using the Jaccard Coefficient (see FAQs) .
• The Homology Panel describes homology relationships taken EnsEMBL compara. The Gene Orthologs table lists genes, which have a homology relation to the gene described (first row: this gene). Using the checkbox users can select a list of genes and display them in a comparative view. In addition genes with orthology relationships have been clustered to a group (cog), which is here displayed as a network graph. This network can be display in different layout, with different parameters, which can be adjusted below the graph.

Gene Compare View

From the gene view a list of ortholgs can be seleced an their expression annotation and images can be compared to each other.

Ontologies

The stage and anatomy ontologies used for expression annotation, can be browsed here.

• Developmental Stage

  Here you can browse the developmental stages of the different species and retrieve more information on them by following the external links. Following the 4DXpress Link you can access the complete entry for a stage including links to all mapped stages in the other species.

• Stage Mapping

  Here you can browse the stage mapping. Developmental stages of each species have been mapped to a list of stages, which is common to all bilateral animals. This facilitates comparisons of developmental time ranges betweeen the different species.

• Anatomy

  Here you can browse the anatomy ontologies of the different species. You can expand or collapse nodes in a tree based representation. You can search for terms by entering text in the search field an press the Find button. With "find next" and "find previous" you can navigate through the hits.