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Data and databases Lars Juhl Jensen EMBL Heidelberg
a lot of data
 
a lot of databases
Duncan Hull, nodalpoint.org
genes and proteins
GenBank
 
 
UniProt
 
 
PDB
 
 
genomes
SGD Saccharomyces Genome Database
 
 
TAIR The Arabidopsis Information Resource
 
 
GeneDB
 
 
Ensembl
 
 
 
and many others
homology
orthology and paralogy
 
InParanoid
model organism databases
 
 
 
HomoloGene
Entrez
 
 
COG Clusters of Orthologous Groups
deep orthology
functional classes
 
OrthoMCL
high resolution
 
 
 
YOGY
meta-database
 
 
eggNOG
multiple resolutions
 
 
 
 
TreeFam
phylogenetic trees
 
 
 
protein domains
CDD Conserved Domain Database
NCBI BLAST
 
 
Pfam
high coverage
 
 
 
SMART
signal transduction
 
 
InterPro
meta-database
 
 
 
structural classification
SCOP
manual assignments
 
CATH
automatic assignments
 
cell cycle
evolution of expression
 
gene expression
microarrays
 
dynamics
GEO Gene Expression Omnibus
 
 
ArrayExpress
 
 
cell cycle
 
 
Cyclebase.org
 
 
 
SCEPTRANS
 
 
interactions
affinity purification
 
yeast two-hybrid
 
synthetic lethality
 
repositories
BioGRID
 
 
DIP Database of Interacting Proteins
 
 
 
IntAct
 
 
MINT Molecular Interactions Database
 
 
 
cell cycle
dynamic network
 
linear motifs
less than 10 residues
 
Prosite
 
ELM
 
Domino
 
 
PepCyber P~Pep
 
 
 
Phospho.ELM
 
 
PhosphoSite
 
 
PhosPhAt
 
 
 
Phosida
 
 
cell cycle
evolution of phosphorylation
 
complexes
CORUM
 
 
Gene Ontology
 
 
cell cycle
regulation of assembly
 
pathways
KEGG
broad coverage
 
 
iPath
 
 
EcoCyc
MetaCyc
metabolism
 
 
Reactome
elegant data model
 
PID Pathway Interaction Database
meta-database
 
 
models
BioModels
 
 
cell cycle
Cyclonet
 
 
 
 
CCDB
 
 
 
 
integration
STRING
 
benchmarking
 
transfer by orthology
 
 
Bayesian framework
 
signaling networks
NetworKIN
 
 
 

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Computational approaches to cell cycle analysis: Data and databases