Biology Reference
In-Depth Information
4.2.3. Proteomics integrated resources
SWISS-2DPAGE is an annotated database developed by the PIG. It
assembles data on proteins from a variety of human and mouse biological
samples as well as from
Arabidopsis thaliana
,
Dictyostelium discoideum
,
Escherichia coli
,
Saccharomyces cerevisiae
, and
Staphylococcus aureus
. In all
cases, proteins have been identified on two-dimensional polyacrylamide
gel electrophoresis (2-D PAGE) reference maps. SWISS-2DPAGE
provides links between sequence data and protein expression. Most
recorded proteins have been identified by one or more methods, including
MS, microsequencing, immunoblotting, gel comparison, or amino acid
composition.
The SWISS-2DPAGE database was the first 2-DE federated database
available on the Internet.
67
Since then, it has been continuously accessible
and expanded,
68
and contains close to 40 maps. Various types of informa-
tion (e.g. genome data, organism-specific data, protein families or
domains, polymorphisms, mutations, structures, metabolic pathways) are
brought together by cross-linking to other resources such as UniProtKB,
PubMed, and other federated 2-DE databases (e.g. HSC-2DPAGE,
PHCI-2DPAGE, Siena-2DPAGE).
The WORLD-2DPAGE List (http://world-2dpage.expasy.org/list/)
is an index to known federated 2-D PAGE databases as well as to 2-D
PAGE related servers and services.
69
It is available from the ExPASy pro-
teomics website and has been continuously updated since 1995. It cur-
rently lists up to 60 databases, totalizing nearly 420 gel images. These
databases are grouped by species and classified into three categories
according to their implementation of some or all of the rules defining a
federated 2-DE database;
70
these rules (http://www.expasy.org/ch2d/
fed-rules.html) have been proposed to facilitate the navigation between
remote databases. In short, a federated 2-DE database has to be accessed
minimally through a keyword search and graphical queries, and also has
to include active links to other related databases.
In the last few years, the accessibility to gel data has not reached
expected levels, and most of the proteomics data are confined in scien-
tific articles or as supplementary material on publishers' websites. In
either case, the data are not fully exploitable for analysis or comparison
