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Welcome to the 2DBase web interface
Important note: This is a modified version of the Make2D-DB II query interface. It is best viewed with Firefox 1.0 (recommended), Opera 8.5 or Internet Explorer 5.0 (or higher versions).
The main objectives of the 2D-PAGE Database of Escherichia coli are:
- to provide the features for query and data-mining applications to access the stored proteomics data
- to efficiently compare the specific protein spots present in the comparable proteome maps
- to analyse the data with the integrated classification for cellular functions of gene products of Escherichia coli (see also GenProtEC references)
This Database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on varios functional categories enabling quick and subsequent analysis. The following section introduces the different features of this interface in more detail.
You can perform simple search queries:
- by accession number: search 2D-PAGE Database of Escherichia coli by accession number or by entry name (AC or ID)
- by description, ID or gene name: search by description (DE), entry name (ID), gene name (GN) or Swiss-Prot keywords (KW)
- by author: search authors list by giving an AC or an ID, or list all entries for a given author
- by spot id / serial number: search by spot ID / serial numbers
- by identification methods: search by identification methods
- by pI/Mw range: search for spots located within a pI/Mw range. You can limit your search to a specific map
You can also perform much more complex queries using the 'combined fields' link.
This option lets you construct your own query by combining various keywords and boolean operators (SRS-like interface).
You can choose the output fields to show and decide to save results as a text file on your own computer.
'proteins in a map' allows you to retrieve in a table all the protein entries identified on a given reference map, with related
2-DE information on spot ID, experimental pI and Mw (read from map), mapping procedures, references, etc..
You can export the table in text format to your computer.
To access the graphical map viewer, use the 'navigate the maps' link.
This viewer lets you navigate and zoom between the different maps. You can display all spots or just show those of particular interest.
By dragging your mouse over the different spots, available
experimental information will be dynamically displayed.
If you want to use the new feature of spot and map
comparison, press the 'compare maps' button.
This
feature enables you to compare and to analyse all spots of two or multiple
maps in a clearly arranged tabular format. At a glance you can check for
example the assigned protein, peak and normalized quantity values and
small image of the spot. Using the newly implemented spot difference scoring function along with the sortable tables you will be able to discover proteomic changes very efficiently. Additionally, you may perform your analysis based on the GenProtEC functional categories (10 main categories) to refine your results. If you want to analyse a functional category in more detail there exists a special functional catagories' browser.
As a member of the fermentation engineering group at bielefeld university you may upload new 2D gel electrophresis experiments using the 'upload new maps' function. A comprehensive 'How to' and help page can be accessed from there.
Unfortunately, we have to disable this feature for other users due to security reasons.
A description of the different experimental procedures of each 2D Gel present in the database can be accessed through the 'materials and methods' link.
This interface has been configured to access several databases. You may select one individual database, or select, simultaneously, several databases for your queries. To select more than one database, use the 'Ctrl' button while clicking on the database name.
This interface has also been configured to automatically access other similar remote interfaces. You may select one or several interfaces for your queries. Please, note that there are some few limitations on queries with remote interfaces (e.g. 'GET' queries will only be run on 'local' databases).
Note also that, by default, there is at least one selected 'local' database. If you want to exclude 'local' databases from your queries (restricting queries to remote interfaces), turn on the 'Exclude local DBs' box.
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