Data and databases

Lars Juhl JensenEMBL Heidelberg

a lot of data

a lot of databases

Duncan Hull, nodalpoint.org

genes and proteins

GenBank

UniProt

PDB

genomes

SGDSaccharomyces Genome Database

TAIRThe Arabidopsis Information Resource

GeneDB

Ensembl

and many others

homology

orthology and paralogy

InParanoid

model organism databases

HomoloGene

Entrez

COGClusters of Orthologous Groups

deep orthology

functional classes

OrthoMCL

high resolution

YOGY

meta-database

eggNOG

multiple resolutions

TreeFam

phylogenetic trees

protein domains

CDDConserved 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

GEOGene Expression Omnibus

ArrayExpress

cell cycle

Cyclebase.org

SCEPTRANS

interactions

affinity purification

yeast two-hybrid

synthetic lethality

repositories

BioGRID

DIPDatabase of Interacting Proteins

IntAct

MINTMolecular 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

PIDPathway Interaction Database

meta-database

models

BioModels

cell cycle

Cyclonet

CCDB

integration

STRING

benchmarking

transfer by orthology

Bayesian framework

signaling networks

NetworKIN