Biology Reference
In-Depth Information
Table 2
URLs for plant proteome databases and Web sites
Arabidopsis thaliana databases
AT_CHLORO
www.grenoble.prabi.fr/at_chloro/
AtPID
www.megabionet.org/atpid/webfi le/
AtProteome
fgcz-atproteome.unizh.ch/
pep2pro
fgcz-pep2pro.uzh.ch/
PhosPhAt
phosphat.mpimp-golm.mpg.de/db.html
SUBA
suba.plantenergy.uwa.edu.au/
TAIR
www.arabidopsis.org/
Rice databases
DIPOS
csb.shu.edu.cn/dipos
OryzaPG-DB
oryzapg.iab.keio.ac.jp/
PRIN
bis.zju.edu.cn/prin/
Rice proteome database
gene64.dna.affrc.go.jp/RPD/
RiceRBP
www.bioinformatics2.wsu.edu/
cgi-bin/RiceRBP/home.pl
Other databases
GabiPD
www.gabipd.org/
Medicago PhosphoProtein DB
phospho.medicago.wisc.edu
P3DB
p3db.org/
plprot
www.plprot.ethz.ch/
PPDB
ppdb.tc.cornell.edu/
PRIDE
www.ebi.ac.uk/pride/
ProMEX
promex.pph.univie.ac.at/promex/
Proteomics of Oilseeds
www.oilseedproteomics.missouri.edu/
Seed Proteome Web Portal
www.seed-proteome.com/
Soybean Proteome Database
proteome.dc.affrc.go.jp/Soybean/
SoyKB
soykb.org/
Web-based tools
GelMap
www.gelmap.de/
iLoc-Plant
www.jci-bioinfo.cn/iLoc-Plant
MRMaid
www.mrmaid.info/
Musite
musite.net/
PASSEL
www.peptideatlas.org/passel/
PredPlantPTS1
ppp.gobics.de/
ProteoRed MIAPE web toolkit
www.proteored.org/MIAPE/
AtPID includes predicted protein-protein interactions for A . thali-
ana [ 17 ]. Interactions are predicted from ortholog interactions,
microarray profi les, GO analyses [ 38 ], conserved domains, and
genomic contexts. The database contains ~28,000 protein-protein
interaction pairs with ~23,000 pairs generated from prediction
methods. The remaining ~5,000 pairs were manually created from
the literature and/or from enzyme complexes in KEGG [ 39 ].
2.1.2 AtPID
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