The LECB 2-D PAGE gel images database is available for public use. It contains data sets from four types of experiments with over 300 gif images with annotation and landmark data in html, tab-delimited and xml formats. It could be used for samples of several types of biological materials and for test data for 2D gel analysis software development and comparison with other similar samples. PAGE is polyacrylamide gel electrophoresis. The LECB was the U.S. National Cancer Institute's Laboratory of Experimental and Computational Biology. Since this work was done, LECB has been reorganized as the CCR Nanobiology Program. The database is available at two Web sites (the bioinformatics.org is the mirror site):
The database consist of four 2D gel image data sets previously analyzed with the GELLAB-II system (also GELLAB-II history). These data consist of over 300 gel images (including some replicate samples and some replicate scans) and are summarized below. The data set experiment conditions are documented in the associated literature references. The four data sets are:
These gel data could be used with the Open2Dprot project (open2dprot.sourceforge.net) software or Flicker gel comparison program (open2dprot.sourceforge.net/Flicker) as well as other 2D gel analysis software such as ImageJ, Photoshop, GIMP, etc.
This data is released for public use under the following conditions listed below (Section 3).
You may view the data directly from the Web site by clicking on hyperlinks in the following (accession and landmark) HTML files to pop up static images in your Web browser (see below). Alternatively, you could compare the images dynamically using the Flicker program on downloaded data sets.
Manually landmarked gel data is also made available. Landmarks are useful in aligning gels in spot pairing software. These are the landmark.tbl, landmark.xml, and landmark.html files. These are vertically stacked spreadsheets. A landmark is a spot position in a reference gel that corresponds to the putatively same spot in another gel - typically matched by flickering the gels to find corresponding local regions. By pairing N-1 gels to a reference gel in a N gel database, it is possible to pair spots back to the reference gel and to build corresponding spot expression lists for analysis. In this data, there are instances where a particular landmark spot is missing from one of the non-landmark gels. This is to be expected in real-world data. The position was estimated by visually aligning neighboring spots in a local region around the landmark in the reference gel with the local region in the other gel. The landmark coordinates should be on the spot since it is assumed that spot matching software will latch onto the actual spot centroid from the manually specified coordinates.
To simplify reading all of the data contained in the accession.tbl and landmark.tbl, we also generated a publish.tbl and publish.xml files which is the relational join of the other two files. It would be used primarily by programs (such as the R program) to read all data about the data set for further analysis.
Finally, the complete set of files including the GIF images is packaged in a project.tar.gz file for each project and may be unpacked with WinZip on Windows PCs, gunzip on Unix, etc.
Human leukemias (AML, ALL, CLL, HCL and other) (Lester, Lipkin, Lemkin). 170 gels [512x512 pixels, 8-bit, 250 microns/pixel, GIF]
References:
HL-60 cell line (Lester, Lipkin, Lemkin). 111 gels
[512x512 pixels, 8-bit, 250 microns/pixel, GIF].
References:
Molt-4 cell line (Lester, Lipkin, Lemkin). Four gels
[512x512 pixels, 8-bit, 250 microns/pixel, GIF].
Fetal Alchohol Syndrome serum biomarkers case-control study
(Robinson, Myrick and Lemkin). 53 gels [512x512 pixels, 8-bit, 340
microns/pixel, GIF]
References:
4. Comparing the images dynamically
It is possible to flicker-compare any two images using the Flicker
program on downloaded data sets. You should:
5. Links to Web sites that have used the data
The following are web sites that use or reference the data.
If you have used the data, send us your links to add to this list.
Go to [LECB (is now CCRNP) |
NCI Home |
Open2Dprot |
Flicker |
Bioinformatics.org
]
$Date: 2006/06/30$ /
P. Lemkin.
lemkin@ncifcrf.gov
or
lemkin@bioinformatics.org