5.9 Pathway Databases 121
occurring in the entire organism (Villanueva et al. 2004). Proteomics data-
bases address five biological questions that cannot be answered by DNA
analysis: (1) the relative abundance of protein products; (2) post-translational
modifications; (3) subcellular localizations; (4) molecular turnover; and (5)
protein-protein interactions (Celis et al. 1998).
HEART-2DPAGE
userpage.chemie.fu-berlin.de/∼pleiss/dhzb.html
Heart High-Performance 2-DE Database
http://www.mdc-berlin.de/∼emu/heart
SWISS-2DPAGE au.expasy.org/ch2d
SIENA-2DPAGE http://www.bio-mol.unisi.it/2d/2d.html
WORLD-2DPAGE us.expasy.org/ch2d/2d-index.html
PMMA-2DPAGE http://www.pmma.pmfhk.cz
RAT HEART-2DPAGE
http://www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d
HSC-2DPAGE http://www.expasy.org/cgi-bin/dbxref?HSC-2DPAGE
Phosphoprotein Database www-lecb.ncifcrf.gov/phosphoDB
REPRODUCTION-2DPAGE
reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi
Toothprint Database biocadmin.otago.ac.nz/tooth/home.htm
COMPLUYEAST-2DPAGE babbage.csc.ucm.es/2d/2d.html
FishProm http://www.abdn.ac.uk/fishprom/index.shtml
Mining of proteome databases can reveal intrinsic patterns and relation-
ships in proteomics data, for example, protein-protein interactions and pro-
tein networks. The identification of patterns in complex proteome data sets
can generate new insights into gene translation and post-translational modi-
fication conditions and can characterize complex biological networks.
5.9 Pathway Databases
Apathwayis a system of molecules (especially proteins) that work together.
Pathways are also called molecular interaction networks, and include meta-
bolic pathways, regulatory pathways, and molecular complexes.
BioPAX http://www.biopax.org/
BioPAX is a collaborative effort to create a data exchange format for biologi-
cal pathway data. The current format is called BioPAX level-1 and represents
metabolic pathway information. Future levels are planned for representing
