Home Genes BLAST Expression Literature About Links
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Home Genes BLAST Expression Literature About Links |
Using CnidomeThe Cnidarian Evolutionary Database links Cnidarian genes with their Cnidarian homologs, bilaterian homologs, and corresponding expression data. Queries can be made on individual genes or expression assays. The Cnidome gene expression advanced query form allows users to query gene expression during Cnidarian development. The database will contain all literature gene expression data from all papers dating back until 1993. If you know of any papers with Cnidarian expression information not in the database, please send a mail to jfryan@bu.edu.
This help document describes the various fields and screens that you will come across while using the Cnidome database.
- Query Form Field Descriptions
- Cnidome Accessions
- Advanced Query Results -- Summary
- Assay Display
- Sequence Display
After entering values in the form fields, click Retrieve to submit the query. Click Reset Form to clear the fields and return any default values.
Query Form Field Descriptions
Field Description Gene Symbol/Name Symbol or name for a Cnidarian genetic marker. Enter one or more symbols or names (each separated by a comma). By default, you search on current symbols/names and synonyms. The synonyms are the synonyms of linked (by phylogenetic analysis) homologous bilaterians. However, you can limit your search to Cnidome accession numbers or GenBank accession numbers.
Cnidome database searching is NOT case sensitive.
Organism Use this field to limit your search to a specific cnidarian species or cnidarian class (Anthozoa, Cubozoa, Hydrozoa, Scyphozoa). Assay type Selection list of assay types. Use this field to limit your search to specific assays. Expression Level The level of expression. Life History Stage Developmental Stage of the tested animal. This is a hierarchical search So a search for Asexual Reproduction will also find results for Asexual Reproduction/Budding, Asexual Reproduction/Fission, etc. Currently you can only limit to a specific life history stage. In the future, you will be able to limit using temporal info (e.g. 1 hour after regeneration). Body Region The region of the body showing (or showing absence of) expression. This is a hierarchical search, so if you search Head you will get results for Head, Head/Hypostome, Head/Hypostome/AroundMouth, etc. Cell Type(s) Cells displaying (or displaying absence of) expresison. Layers Layers of the body where expression was (or wasn't) detected. Cnidome Accessions
All Sequences, Assays, and Assay Results have been assigned unique accession numbers. Each category has its own prefix
Prefix Type Of Record Cns Sequence Cnx Expression Assay Cnr Expression Assay Result Advanced Query Results -- Summary
The results for a Gene Expression Search is a list of expression assays that match your search critia. An expression assay result consists of a Cnidome accession for the assay. The type of assay peformed. The PubMed ID of the literature from which the assay was extracted. The Cnidome accession of the sequence used in the expression assay. The name of the sequence and the corresponding organism.
Assay Display
When you click on a Cnidome expression assay accession, it takes you to an Expression Results page. This displays all the expression information extracted from an individual assay. The first column displays the Cnidome expression result accession number. This column is followed by the details of the expression result: layers, body region, life history state, cell type, expression level, and temporal info.
Sequence Display
When you click on a Cnidome sequence accession, it takes you to a Sequence Results page. This displays the Cnidome accession number, The Genbank accession number, the name of the sequence, the definition line taken from the GenBank record. If it exists a table of homologous bilaterian information is displayed. In addition a list of homologous Cnidarian sequences are displayed if there are known homologues in the database. Finally a list of Expression assays that have this sequence is involved with.