Comparing 2-D electrophoretic gels across Internet databases.

Abstract

In ref. , we described a computer-assisted visual method, Flicker, for comparing two two-dimensional (2-D) protein gel images across the Internet is described (see Note 5). This approach may be useful for comparing similar samples created in different laboratories to help putatively identify or suggest protein spot identification. 2-D gels and associated databases are increasingly appearing on the Internet (, , , , , , , , , , , ) in World-Wide Web (WWW or web) () servers and through federated databases (). Table 1 lists some web URL addresses for a number of 2-D protein gel databases that contain 2-D gelimages with many identified proteins. This opens up the possibility of comparing one’s own experimental 2-D gel image data with gel images of similar biological material from remote Internet databases in other laboratories. This new data analysis method allows scientists to collaborate and compare gelimage data over the World Wide Web more easily. Table 1 Partial List of WWW 2-D Electrophoretic Gel Databases ExPASy (liver, plasma, CSF, and so forth, SWISS-2DPAGE), http://expasy.hcuge.ch/Argonne Protein Mapping Group (mouse liver, human breast cell lines),http://www.anl.gov/CMB/PMG/ Heart Science Centre, Harefield Hospital (Human Heart 2D gel Protein DB),http://www.harefield.nthames.nhs.uk/ Berlin Human Myocardial 2-D Electrophoresis Protein Database,http://www.chemie.fu-berlin.de/user/pleiss/Cambridge 2-D PAGE (rat neuronal Database),http://sunspot.bioc.cam.ac.uk/NEURON.html Embryonal Stem Cells (Immunobiology, University of Edinburgh), http://www.ed.ac.uk/ simnh/2DPAGE.html Human Colon Carcinoma Protein Database (Joint Protein Structure Lab),http:// www.ludwig.edu.au/www/jpsl/jpslhome.html Keratinocyte database (Danish Centre for Human Genome Research), http://biobase.dk/cgi-bin/celis/ CSH QUEST Protein Database (yeast, REF52 rat, mouse embryo), http://siva.cshl.org/ E. coli Gene-Protein Database Project-ECO2DBASE (in NCBI repository) http://pcsf.brcf.med.umich.edu/eco2dbase/ Yeast 2D-PAGE, http://yeast-2dpage.gmm.gu.se/ Large-Scale Biology Corp (2-D maps: rat, mouse and human liver), http://www.lsbc.com/patterns.htm PROTEOME Inc (YPD-Yeast Protein Database), http://www.proteome.com/YPDhome.html NIMH-NCI Protein Disease Database (PDD) (plasma, CSF, urine), http://www-pdd. ncifcrf.gov/ Itemize a Individual gel images with identified proteins are available in these databases. The user should investigate them individually since URL paths for 2D gel image files will differ.