Results of 2DWG Web Gel Meta-Database Search


The search results in the table below is a subset of the 2DWG meta-database of 2D gel images found on the Internet.


List of 2D gel images

Search expression: Human AND Map AND Lung

There was 0 entries found matching the query.


Flicker Comparison of gels in this table

The NCI Flicker program is a Java application running on your web browser for visually comparing images over the Internet. You can flicker compare a gel image residing on your computer with one of the images in this table. See the form entries below.

NOTE: In addition, you can flicker data from the entire 2DWG database table. However, you must go to a separate web Page to pick two gels from separate lists of gels or arbitrary URLs.

In these databases, some images are reversed in the horizontal pI direction and others may be reversed in Mr in the vertical direction. Flicker will let you transform an image with the Flip Horiz and Flip Vert operations to flip an image in the horizontal and vertical dimensions. Because some images are on a larger scale (either through the way they were run or because of the scanner resolution), you might consider using the Affine Transform option to make the regions being compared have similar scale. The Flicker Reference Manual contains additional information on running Flicker.


Select 2D gels to Flicker Compare:
exactly two gels by selecting Image URL checkboxes in the above table or,
select one gel from the table and enter the other as an image URL (http:// or ftp://)
Image URL:

Canvas Size, Use JavaPlugin


Notes on the 2DWG Meta-database of 2D gel images

This 2DWG a catalog of some of the 2D gel images found in a search of 2D gel databases on the web. We will be refering to this catalog as the "2DWG" meta-database. A meta-database contains information about data in other databases. Data for the 2DWG is acquired by a conbination of review of results from web searching as well as submissions by web database authors. The image files are generally in GIF, JPEG or TIFF file formats which are suitable for Web browsers. The table is organized by tissue type to make it easier to find data on the same tissue from different web sources. Note, you can search 2DWG by keywords to generate specific subtables. This is much faster than scrolling the entire 2DWG catalog.

The table is organized as a spreadsheet with column headings at the top. Each row corresponds to a gel image with the fields in the row describing the gel. The fields are defined in the Glossary of fields.

Hint: because the table is very wide, you might want to increase the width of your browser (it looks best with Netscape). Note also that the Miscellaneous column has information in a smaller font. This is hard to read with 72 dots-per-inch displays, but when printed on a 300DPI or better printer it is quite readable.

Each table entry is defined with a database name in the Image URL (eg. a plasma gel image), DB URL which indicates where the image came from in the web server (eg. the page describing the plasma gel), a link to the related web organization server, (eg. "ExPASy") where more information might be found on the sample, the methods, etc. In addition, some of the servers have spot maps identifying the proteins in these gel images, so the Map URL is also put into a table entry if it exists. Otherwise, it is defined to be a raw gel image. These may be passive or active, with the latter leading back into protein identification databases residing on these other servers. While most gel images have pI oriented acid to basic, some gels are reversed. We indicate this where possible by specifying the pIe range as increasing (acid to basic, eg. 4-8) or decreasing (basic to acid, eg. 8-4). Since many of these databases are being improved, you can expect these entries to change with some images being deleted and new ones added or replaced.

You may flicker compare these gels on the web using the NCI Flicker server.

This catalog will be continuously revised and edited. If you have corrections or additions to this table, or know of published 2D Web gels you think should be included, or have other suggestions to make the table easier to use or more relevant, contact Peter Lemkin (Ed), NCI/FCRDC by E-mail at lemkin@ncifcrf.gov. You will notice that some of the fields in the table are empty. In many of the web databases, this information is missing or not apparent. We will be working to resolve as much of this missing data as possible.

Glossary of column headings used in the 2DWG table

Tissue or Organelle
Tissue or organelle of origin of sample. If there are subcategories, they are appended to the right (eg. lymphocyte-T, etc.)
Species
Species of the sample.
Cell line (strain)
Cell line or strain of sample if applicable.
Image URL
URL to the gel image. Currently ftp:// and http:// protocols and GIF, JPEG or TIFF images are accepted.
DB URL
URL to the specific database where this image resides and which may discuss this data in more detail. This database may also include spot maps of identified proteins.
Isotope / stain / Ab
Detection method. Typically isotope implies autoradiographs or phosphor-imaging (in which case the radioisotope is mentioned, eg. 35[S]-met); stain (eg. Coomassie Blue or silver for silver stain); and Ab is antibody (eg. anti-PY, anti-p53, etc.).
CA/IPG
First dimension method: Carrier Ampholytes or Immobilized pH Gradients.
IEF/NEPHGE
Type of gel: IsoElectric Focusing or Non-Equilibrium PH Gradient Electrophoresis.
pH range
The isoelectric pH range if known. If the range is specified as 8-4, then this means that acid is on the right, the default is acid is on the left (eg 4-8).
Mr (Kd) range
The Molecular Mass range if known. If the range is specified with "mwm", this indicates that molecular weight markers are used to specify the range.
Lab/ Org/ Comp
The name of the Laboratory, Organization or Company where the web database resides. This entry is linked to thetop level web page for that organization.
Scan/synth/diagrm
Whether the image is a scan of a single gel, a composite of a number of gels, a synthetic gel, or a diagram of spot positions.
Map/raw data
Whether the image is a raw gel image or a spot map (with proteins identified by name or number indices used by the particular DB scheme). If a URL is available for the spot map, then it is provided. Note that for some databases although a map exists, you must track down the spot mapping of numbers to protein identifications in associated papers. In other databases, there are active gel images where the user can click on an image to look up the database contents (if any) for that spot.
Miscellaneous
Additional information about the gel, sample, etc. This should complement the other fields so the entry is sufficient to identify the material.
2DWG ID #
Identification number WG00001, WG00002, ... for the 2DWG database assigned by the 2DWG during the submission process.



2dwgDB search performed: 10/06/2008, 09:44:52PM

Peter Lemkin (Ed), lemkin@.ncifcrf.gov
dbEngine program: $Revision: 2.25 $ / $Date: 1999/03/16 22:58:06 $
DB: 2DWG $Revision: 1.50 $ / $Date: 2000/01/21 19:16:53 $ / lemkin@ncifcrf.gov