ABSTRACT
SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The current release contains 343 entries of human, yeast (
Saccharomyces cerevisiae
) and
Escherichia coli
origin, as well as virtual entries for each of the protein sequences in the
SWISS-PROT database.
SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), created and maintained at the University Hospital of
Geneva in collaboration with the Department of Medical Biochemistry of Geneva
University (
1
,
2
). The proteins have been identified on various 2-D PAGE reference maps by microsequencing, immunoblotting, gel comparison and amino acid composition.
Each entry in the SWISS-2DPAGE database corresponds to one protein and contains textual as well as
image data. A sample entry is shown in Figure
1
. The textual part of the database follows the conventions used in the SWISS-PROT protein sequence database (
3
). The identification (ID) and the accession (AC) number are the same as the
corresponding sequence entry in SWISS-PROT. The description (DE) line contains general descriptive information
about the protein. The reference lines (RN, RP, RC, RX, RA and RL) contain
bibliographical references. Each entry also holds a database cross-reference (DR) line pointing to the related SWISS-PROT entry, as well as to related entries in other 2-D PAGE databases, such as YEPD for
Saccharomyces cerevisiae
(
4
) and ECO2DBASE for
Escherichia coli
(
5
). Three line types are specific to SWISS-2DPAGE: (i) the master (MT) line lists what types of maps the protein has
been identified on (examples are LIVER and PLASMA); (ii) the images (IM) line
lists the 2D PAGE images which are associated with the entry (for example TUMOR
LIVER or NORMAL LIVER); (iii) the 2-dimensional gel (2D) line gives specific information such as mapping
procedure (matching with another gel, microsequencing, etc.), the number,
molecular weight and pI of spots and their amino acid composition or describes
normal and pathological variants (
6
,
7
).
SWISS-2DPAGE is currently available on the ExPASy World Wide Web (WWW) molecular
biology server (
8
). To access this server (or any other WWW server) one needs a WWW browser.
Public domain browsers exist for a variety of computer systems, including Unix,
MS Windows and the Macintosh operating system. Popular browsers available for
all three platforms include Mosaictm, developed at the National Center for Supercomputing Applications (NCSA)
of the University of Illinois at Champaign (obtainable by anonymous ftp from
ftp.ncsa.uiuc.edu), and Netscape Navigatortm, from Netscape Communications Corp. (available from ftp.netscape.com).
Using a WWW browser one has access to all the hypertext documents stored on the
ExPASy server (as well as other WWW servers).
The ExPASy WWW server may be accessed through its Uniform Resource Locator (URL,
the addressing system defined in WWW), which is http://expasy.hcuge.ch/.
A SWISS-2DPAGE entry may be obtained from the server in one of three ways. (i) By
keyword search on the protein name, accession number or referenced author. (ii)
From a SWISS-PROT entry, by selecting the hypertext link in the cross-reference (DR) line to SWISS-2DPAGE. If no corresponding entry exists in SWISS-2DPAGE a virtual entry is created, from which one may
view any of the 2-D PAGE reference maps. The theoretical pI and molecular weight for the
protein are computed and its position is shown on the map. (iii) By selecting a spot on one of the 2-D PAGE reference maps.
The current release contains 343 entries of human, yeast and
E.coli
origin, as well as virtual entries for each of the protein sequences in the
SWISS-PROT database. SWISS-2DPAGE entries are linked to reference 2-D PAGE maps. Maps for the following biological samples are
available: human liver, plasma, HepG2, HepG2 secreted proteins, red blood cell,
lymphoma, cerebrospinal fluid, macrophage-like cell line, erythroleukaemia cell and platelet, as well as yeast (
S.cerevisiae
) and
E.coli
.
REFERENCES
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