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120 5 Survey of Ontologies in Bioinformatics

for transcriptional expression. These databases can be used for both hypoth-

esis testing and knowledge discovery.

NCBI’s dbEST Database http://www.ncbi.nlm.nih.gov/dbEST/

The GeneCards Database

bioinformatics.weizmann.ac.il/cards

Kidney Development Gene Expression Database

organogenesis.ucsd.edu

Gene Expression in Tooth bite-it.helsinki.fi

Mouse Gene Expression Database http://www.informatics.jax.org

The Cardiac Gene Expression Knowledgebase

http://www.cage.wbmei.jhu.edu

Gene Expression Atlas expression.gnf.org/cgi-bin/index.cgi

NCBI’s Gene Expression Omnibus

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo

Cancer Gene Expression Database

cged.hgc.jp/cgi-bin/input.cgi

SaccharomycesGenome Database http://www.yeastgenome.org

The Nematode Expression Pattern DataBase

nematode.lab.nig.ac.jp

WormBase http://www.wormbase.org

ThePlasmodiumGenome Resource plasmodb.org

The Zebrafish Information Network zfin.org

5.8.2 Proteomics Databases

Proteomicsis defined as the use of quantitative protein-level measurements of

gene expression to characterize biological processes and elucidate the mech-

anisms of gene translation. The goal of proteomics is the quantitative mea-

surement of protein expression in various conditions such as under the in-

fluence of a drug or being in a specific disease condition. There are gener-

ally two steps in proteomics - protein separation and protein identification.

Protein separation is usually performed using 2D polyacrylamide gel elec-

trophoresis (2D-PAGE). Protein identification is usually accomplished using

Edman degradation, mass spectrometry, or Western blotting. Protein quan-

tification can be achieved through radiolabeling and scanning or phospho-

imaging. Proteomics is important in disease diagnosis and prognosis. For

example, human serum contains a spectrum of proteolytically derived pep-

tides (serum peptidome) that may provide a correlate of biological events