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- Navigating Casbase. Below shows a screenshot
of a section of the homepage. The navigation bar at the top of
the page indicate the various sections on the website. The "about
casbase" link will direct users to the homepage which introduces
the database objectives and contents. The "query caspase"
and "query substrates" links will direct users to the
query pages for retrieving data on caspases and their substrates
respectively. The "research" link leads to a page listing
various caspase and/or apoptosis research groups. The "contact"
link provides contact information.
- Querying for caspases and substrates. Below
shows the screenshot of a query page for caspases. A similar page
exist for queries on caspase substrates. In both query pages,
users can search the database using various methods: a) Using
Accession IDs -such as the Casbase Accession IDs or Uniprot (Swiss-Prot/TrEMBL)
IDs. b) Using Keywords (synonyms, common protein names, gene names).
c) Using BLAST (a protein sequence can be submitted into the text
box and a similarity search for caspases and their substrates
can be made.
- Search Results. The
screenshot below shows a typical results page of a query for both
caspases and caspase substrates (only caspase search results page
is shown) using keyword "caspase-3" with no organism
type selection. Users can click on the casbase accession IDs of
each record to view a detailed page of the record.
- Detailed page of a caspase record. Below shows
the screenshot of a detailed page of a caspase record (caspase-3
human from clicking of the link in the results page). It shows
the Casbase Accession ID, the caspase's name, the organism source,
the accession ID from Swiss-Prot/TrEMBL(hotlinked to the relevant
entry at Uniprot), the gene name, synonyms, Interpro domain organization
(linked to the Interpro entry), PDB structures (if available,
and is hotlinked if there's any), sequence information (can be
downloaded as FASTA formatted sequence) and comments.
- Detailed page of a substrate record (example: gelsolin). Below
shows the detailed page of a substrate record.
Comments on the various fields:
Casbase Accession ID: Reports the accession number used internally
by Casbase.
Substrate Name: Name of substrate.
Organism Type: Organism source of entry.
GO Process and GO-function: Gene Ontology terminology is used
for describing the function of proteins.
Cleavage Site(s): the tetrapeptide sequence which is recognized
by caspases. Usually the last residue is an aspartate. The number within parentheses
indicate the position of the first residue of the tetrapeptide sequence on the protein.
Cleavage Effect(s): The consequences of cleavage of substrates.
on cellular physiology/function
Caspase(s) Involved: indicates the caspase or caspases responsible for cleavage.
Comments: Addtional comments/information on the substrate.
Sequence: users can download the sequence in FASTA format.
References: Literature from which the substrate information was taken from.
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