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2010 NAR Database Summary Paper


Nucleotide Sequence Databases
International Nucleotide Sequence Database Collaboration
DDBJ - DNA Data Bank of Japan
European Nucleotide Archive
GenBank®
Coding and non-coding DNA
ACLAME - A Classification of Mobile genetic Elements
Ciliate IES-MDS database
CORG - A database for COmparative Regulatory Genomics
CUTG - Codon Usage Tabulated from GenBank
DiProDB
ECRbase
FREP
Genetic Codes
GISSD
GyDB
HumHot
InSatDb
Isfinder
Islander
L1Base
MethDB
MICdb - Database of Prokaryotic Microsatellites
NPRD - Nucleosome Positioning Region Database
OriDB - The DNA Replication Origin Database
PANDIT
Patome
PolymiRTS
PseudoGene
RECODE
RefSeq
RegTransBase
RetrOryza
S/MARt DB
SNPSTR
STRBase
Synthetic Gene Database
TassDB
TIGR plant repeat database
TIGR Plant Transcript Assembly database
TransoGene
TRDB
UCbase and miRfunc
UgMicroSatdb
UniVec
UTRdb/UTRsite
UTRome
VectorDB
VISTA Enhancer Browser
Gene structure, introns and exons, splice sites
ARTADEdb
ASAP II
ASDB - Alternative Splicing Database
ASHESdb
ASTD
ChimerDB
ECgene
EDAS - EST-Derived Alternative Splicing Database
EID: Exon-Intron Database
ExInt
ExtraTrain
FESD - Functional Element SNPs Database
FUGOID
H-DBAS
Hollywood
HS3D - Homo Sapiens Splice Sites Dataset
Intronerator
ProSAS
SpliceDB
SpliceInfo
SpliceNest
U12DB
Xpro
Yeast Intron Database
Transcriptional regulator sites and transcription factors
ABS
ACTIVITY
AGRIS - Arabidopsis Gene Regulatory Information Server
ASPD
Cancer Chromosomes
cisRED
CMGSDB
CoryneRegNet
COXPRESdb
CTCF Binding Site Database
DBD
DBTBS
DBTSS
DoOP - Databases of Orthologous Promoters
DPInteract
ECRbase
EPD
FlyTF
GeneNet
GenomeTraFaC
Greglist
HTPSELEX
JASPAR
MachiBase
MAPPER
MPromDB
ODB - Operon database
ooTFD
ORegAnno
Osteo-Promoter Database
PAZAR
PLACE
Plant Stress-Responsive Gene Catalog
PlantCARE
PlantProm
PPDB: Plant Promoter Database
PReMod
PRODORIC
PromEC
ProTISA
PTM-Switchboard
QuadBase
REDfly
RegulonDB
rSNP Guide
SCPD - Saccharomyces cerevisiae promoter database
SELEXdb
SKY/M-FISH and CGH
SwissRegulon
Telomerase database
TESS
TiProD
TRACTOR db
TRANSCompel®
TRANSFAC®
TransfactomeDB
TRANSPATH®
Transterm
TRED - Transcriptional Regulatory Element Database
TRRD
TrSDB
UniPROBE
VISTA Enhancer Browser
YEASTRACT
RNA sequence databases
16S and 23S Ribosomal RNA Mutation Database
3D rRNA modification maps
5S Ribosomal RNA Database
Aptamer Database
ARED
Argonaute
BPS
Cereal Small RNA Database
CORG - A database for COmparative Regulatory Genomics
dbRES
European rRNA database
FlyRNAi
fRNAdb
Greengenes
GRSDB
GtRDB - Genomic tRNA Database
HIV Sequence Database
HuSiDa - Human siRNA database
Intronerator
IRESdb - the Internal Ribosome Entry Site database
IRESite
ITS2
MeRNA
microRNA.org
miR2Disease
miRBase
miRecords
miRGator
miRGen
miRNAMap
miROrtho
Mobile group II introns database
MODOMICS
NATsDB
NCIR - Non-Canonical Interactions in RNA
ncRNAs database
NONCODE
NPInter
NRED
piRNABank
Plant snoRNA DB
PLMItRNA
PolyA_DB
PseudoBase
REDIdb
Rfam
Ribosomal Database Project (RDP-II)
RISSC - Ribosomal Internal Spacer Sequence Collection
RNA FRABASE
RNA Modification Database
RNA SSTRAND
RNAdb
RNAi codex
RNAJunction
SELEXdb
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data
siRecords
siRNAdb
Sno/scaRNAbase
snoRNA-LBME-db
sRNAMap
SRPDB
Subviral RNA Database
TarBase
The Small Subunit rRNA Modification Database
The tmRNA website
tmRDB
tRNA Sequences
tRNADB-CE
UTRdb/UTRsite
Vir-Mir db
Yeast snoRNA Database
Protein sequence databases
General sequence databases
EXProt
MIPS resources
NCBI Protein database
PA-GOSUB
Patome
PIR - Protein Information Resource
PRF
RefSeq
Swiss-Prot (UniProtKB\Swiss-Prot)
TCDB
UniParc
UniProt
UniRef
UniSave
Protein properties
AAindex
BindingDB
Cybase
dbPTM
iProLINK
KDBI
MALISAM
MegaMotifbase
PFD - Protein Folding Database
PIDD
PINT
PPD
PPT-DB
ProTherm
PRTAD
REFOLD
Protein localization and targeting
CentrosomeDB
DBSubLoc - Database of protein Subcellular Localization
eSLDB - eukaryotic Subcellular Localization database
InterFil
LOCATE
MiCroKit
MitoRes
NESbase
NLSdb
NMPdb - Nuclear matrix associated proteins database
NOPdb: Nucleolar Proteome Database
NPD - Nuclear Protein Database
Nuclear Receptor Resource
NUREBASE
NURSA
OGRe - Organellar Genome Retrieval
PeroxisomeDB
PSORTdb
Secreted Protein Database
SUBA
THGS - Transmembrane Helices in Genome Sequences
TopDB
TransMembrane Protein DataBase
Protein sequence motifs and active sites
ASC - Active Sequence Collection
Blocks
CoC Central
COMe - Co-Ordination of Metals etc.
CoPS
CSA - Catalytic Site Atlas
eBLOCKS
eF-site - Electrostatic surface of Functional site
FireDB
InterPro
Metalloprotein Site Database
Minimotif Miner
O-GLYCBASE
PDBSite
Phospho.ELM
Phospho3D
PRINTS
PROMISE
ProRule
PROSITE
ProTeus
SDR
SitesBase
SuperSite
TMFunction
Protein domain databases; protein classification
ADDA - A Domain Database
BAliBASE
Benchmark
BIOZON
CDD
CluSTr
COG - Clusters of Orthologous Groups of proteins
DomIns - Database of Domain Insertions
eggNOG
EPGD
EVEREST - EVolutionary Ensembles of REcurrent SegmenTs
FunShift
FusionDB
Hits
InterDom
InterPro
iProClass
MulPSSM
OPTIC
OrthoDB
PairsDB
PALI
PANDIT
PANTHER
Pfam
PhyloFacts
PIRSF
ProDom
Protein Clusters
Protein Segment Finder
ProtoNet
SBASE
SIMAP
SISYPHUS
SMART
SUPFAM
TCDB
TIGRFAMs
Databases of individual protein families
ABCdb
Aminoacyl-tRNA synthetase database
Animal Toxin Database
ARAMEMNON
BACTIBASE
BANMOKI
CAZy
ChromDB
cpnDB
CREMOFAC
CSDBase - Cold Shock Domain database
CyMoBase
DB-PABP
DCCP - Database of Copper-Chelating Proteins
Defensins Knowledgebase
Degradome Database
DExH/D Family Database
DSD
Endogenous GPCR List
EROP-Moscow
ESTHER
FCP
FUNPEP
GPCR NaVa database
GPCRDB
gpDB - G-protein database
Heme Protein Database
Histone Database
HIV RT and Protease Sequence Database
Homeobox Page
Homeodomain Resource
InBase
Kinomer
Knottin database
LGICdb
Lipase Engineering Database
Lipid MAPS
LOX-DB
MEROPS
NORINE
Nuclear Receptor Resource
NucleaRDB
NUREBASE
NURSA
OKCAM
Olfactory Receptor Database
Peptaibol
PeroxiBase
PHYTOPROT
PLANT-PIs
PlantsP/PlantsT
PlantTFDB
PlantTribes
PLPMDB
ProLysED - Prokaryotic Lysis Enzymes Database
Protein kinase resource
REBASE
Ribonuclease P Database
RNRdb
RPG - Ribosomal Protein Gene database
RTKdb - Receptor Tyrosine Kinase database
SDAP
SelenoDB
SENTRA
SEVENS
SRPDB
SysZNF
Telomerase database
TransportDB
UCSD-Nature Signaling Gateway Molecule Pages
VKCDB - Voltage-gated K+ Channel Database
Wnt Database
ZiFDB
Structure Databases
Small molecules
AANT - Amino Acid - Nucleotide interaction database
ChEBI - Chemical Entities of Biological Interest
ChemBank
ChemDB
CSD - Cambridge Structural Database
DrugBank
Het-PDB Navi
HIC-Up
Klotho
LIGAND
MMsINC
PDB-Ligand
PubChem
R.E.DD.B.
SuperDrug
SuperNatural
SuperScent
SuperToxic
Carbohydrates
BCSDB/Glycoscience
CCSD - Complex Carbohydrate Structure Database (CarbBank)
CSS - Carbohydrate Structure Suite
Glycan
Glycoconjugate Data Bank
GlycoMapsDB
GlycoSuiteDB
Monosaccharide Browser
SWEET-DB
Nucleic acid structure
Greglist
GRSDB
ITS2
MeRNA
NCIR - Non-Canonical Interactions in RNA
NDB
NTDB
QuadBase
Rfam
RNA FRABASE
RNA SSTRAND
RNAJunction
SARS-CoV RNA SSS
SCOR - Structural Classification Of RNA
Vir-Mir db
Protein structure
3D-Genomics
3DID - 3D interacting domains
ArchDB
AS-ALPS
ASTRAL
AutoPSI
BANMOKI
BioMagResBank
CADB - Conformational Angles DataBase of Proteins
CATH
CC+
CE
CoC Central
ColiSNP
Columba
ConSurf-DB
CPDB
CSA - Catalytic Site Atlas
Dali database
DBAli
Decoys-R-Us
DisProt - Database of Protein Disorder
DMAPS
Dockground
DomIns - Database of Domain Insertions
DSDBASE - Disulfide Database
DSMM - a Database of Simulated Molecular Motions
eF-site - Electrostatic surface of Functional site
EzCatDB
FireDB
FSN
Gene3D
Genomic Threading Database
GTOP - Genomes To Protein structures
HOMSTRAD - Homologous Structure Alignment Database
HotSprint
IMGT/3Dstructure-DB
IMOTdb
JAIL
Jenalib: Jena Library of Biological Macromolecules
KineticDB
LPFC
MALISAM
MegaMotifbase
MMDB
ModBase
MolMovDB - Database of Macromolecular Movements
PASS2
PDB
PDB-REPRDB
PDBe
PDBselect
PDBsum
PDB_TM
PFD - Protein Folding Database
Phospho3D
PIDD
piSite
PMDB - Protein Model Database
ProSAS
PROTCOM
PRTAD
PSI-SGKB
RESID
RsiteDB
S4: Structure-based Sequence Alignments of SCOP Superfamilies
SCOP - Structural Classification Of Proteins
SCOPPI
SISYPHUS
SitesBase
SNAPPI
SPROUTS
SSToSS - Sequence-Structural Templates of Single-member Superfamilies
STINGreport
Structure Superposition Database
SUPERFAMILY
SURFACE
SWISS-MODEL Repository
TargetDB
TMBETA-GENOME
TOPOFIT-DB
TOPS - Topology Of Protein Structures
VIPERdb
Voronoia
Genomics Databases (non-vertebrate)
MGD - Mouse Genome Database
TIGR Gene Indices
Genome annotation terms, ontologies and nomenclature
BioThesaurus
FunSimMat
GO - Gene Ontology
GOA - Gene Ontology Annotation
GOPaD
HGNC Database
IUBMB Nomenclature database
IUPAC Nomenclature database
IUPHAR-RD
Plant Ontology database
SOURCE
TreeBase
Taxonomy and identification
GeneTrees
IDBD
MICdb - Database of Prokaryotic Microsatellites
NCBI Taxonomy Browser
Ribosomal Database Project (RDP-II)
RIDOM - Ribosomal Differentiation of Medical Microorganisms
RISSC - Ribosomal Internal Spacer Sequence Collection
Selectome
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data
SuperCAT
Tree of Life
General genomics databases
Animal Genome Size Database
BacMap
Biodefense Proteomics Resource Center
COG - Clusters of Orthologous Groups of proteins
CoGenT++
DEG - Database of Essential Genes
diArk
EBI Genomes
eggNOG
Entrez Gene
Entrez Genomes
EPGD
ERGO-Light
GenDiS
GeneNest
GenoList
Genome information broker
Genome Project Database
Genome Reviews
GOLD
GtRDB - Genomic tRNA Database
HOINVGEN
Inparanoid
Integr8 (formerly Proteome Analysis Database)
KaryotypeDB
KEGG - Kyoto Encyclopedia of Genes and Genomes
MBGD - Microbial Genome Database
MeGX
MetaCyc
Narcisse
NegProt - Negative Proteome database
NMPDR - National Microbial Pathogen Data Resource
OrthoMCL
ParameciumDB
PartiGeneDB
PEDANT
PEP: Predictions for Entire Proteomes
PhylomeDB
PUMA2
STRING
TDRtargets
TIGR Comprehensive Microbial Resource
TIGR Gene Indices
TMBETA-GENOME
TransportDB
Viral genome databases
BioHealthBase
CoVDB
DPVweb
euHCVdb
HCV Database
HCVDB - Hepatitis C Virus Database
HepSeq
HERVd - Human Endogenous Retrovirus database
HIV Drug Resistance Database
HIV Interactions database
HIV Molecular Immunology Database
HIV RT and Protease Sequence Database
HIV Sequence Database
Influenza Virus Resource
ISED
IVDB - Influenza Virus Database
NCBI Viral genomes
Poxvirus.org
RNA Virus Database
SARS-CoV RNA SSS
Subviral RNA Database
T4-like genome database
The HIV Positive Selection Mutation Database
VIDA
VIPERdb
Viral Bioinformatics Resource
VirGen
ViTa
Prokaryotic genome databases
EchoBASE
ShiBase
AlterORF
ARDB
ASAP - A Systematic Annotation Package
ATGC
BSORF - Bacillus subtilis Open Reading Frames
BuchneraBase
CCDB - The CyberCell Database
CIDB - Chlamydia Interactive Database
CMGSDB
coliBase
Colibri
Comparative Genometrics
CoryneRegNet
CyanoBase
DBTBS
DOOR
DPInteract
EcoCyc
EcoGene
EMGlib - Enhanced Microbial Genomes Library
Ensembl Genomes
ERIC
Essential genes in E. coli
FusionDB
GeneDB
GenoBase
GenomeAtlas
GenProtEC
HAMAP
HEG-DB
HGT-DB, Horizontal Gene Transfer-DataBase
IMG Genomes
IMG/M
Interrupted coding sequences
Isfinder
Islander
LEGER
LeptoList
Metagrowth
MolliGen
MtbRegList
MvirDB
NRSub
ODB - Operon database
OperonDB
PAIDB - Pathogenicity Island Database
PATRIC
PEC - Profiling of E. coli Chromosome
PGTdb - Prokaryotic Growth Temperature database
PromEC
ProTISA
Pseudomonas Genome Database
RegTransBase
RegulonDB
Roundup
RRNDB
RsGDB
SIDDBase
Strepto_DB
SubtiList
Sulfolobus
SYSTOMONAS
TBDB
UCSC Archaeal Genome Browser
VFDB - Virulence Factors Database
VNTR Locus Database
xanthusBase
Unicellular eukaryotes genome databases
ApiDB - Apicomplexan DataBase
ApiDots
Aspergillus Genomes
Comparasite
CryptoDB - Cryptosporidium database
Diatom EST Database
DictyBase
Ensembl Genomes
Full-Malaria
GeneDB
GiardiaDB.org
metaTIGER
PlasmoDB
ProtozoaDB
TBestDB
TcruziDB
TcSNP
TGD - Tetrahymena Genome Database
ToxoDB - The Toxoplasma gondii Genome Database
U-genome
Fungal genome databases
Magnaporthe grisea Database
AGD - Ashbya Genome Database
CADRE - Central Aspergillus Data Repository
Candida Genome Database
CandidaDB
CFGP
COGEME Phytopathogenic Fungi and Oomycete EST Database
CYGD - Comprehensive Yeast Genome Database
Ensembl Genomes
FGDB
Fungal Genome Size Database
Génolevures
GermOnline
MNCDB
Mpact
OGD - Oomycete Genomics Database
OriDB - The DNA Replication Origin Database
PHI-base
PROPHECY
SCMD - Saccharomyces cerevisiae Morphological Database
SCPD - Saccharomyces cerevisiae promoter database
SGD - Saccharomyces Genome Database
TRIPLES
VBI Microbial Database
YDPM - Yeast Deletion Project
Yeast Intron Database
Yeast Resource Center
Yeast snoRNA Database
YEASTRACT
YGOB
yMGV - Yeast microarray global viewer
YMPD
Invertebrate genome databases
Drosophila microarray centre
ACeDB
AphidBase
AppaDB
BeetleBase
ButterflyBase
C. elegans Project
CIPRO
CnidBase
Comparasite
CuticleDB
Drosophila polymorphism database
DroSpeGe
Ensembl Genomes
FLIGHT
FlyBase
FlyBrain
FlyEx
FlyMine
FlyRNAi
FLYSNP
FlyTF
FlyTrap
FlyView
GadFly
GeniSys
GenomeRNAi
HOINVGEN
Homophila
InSatDb
InterActive Fly
Intronerator
KinG
LumbriBASE
MapViewer
MitoDrome
Nematode.net
NEMBASE
PPNEMA
Pristionchus.org
REDfly
RNAiDB
SchistoDB
Sebida
SilkDB
SilkSatDb
SmedGD
SpodoBase
StellaBase
UTRome
VectorBase
wFleaBase
WorfDB - Worm ORF Database
WormBase
WormBook
Metabolic and Signaling Pathways
Enzymes and enzyme nomenclature
BindingDB
BRENDA
ENZYME
Enzyme Nomenclature
ExplorEnz
FCP
IntEnz
MACiE
ORENZA
PRECISE
PROCOGNATE
SCOPEC
TECRdb
Metabolic pathways
BioCarta
BioCyc
Bionemo
BioSilico
BRITE - Biomolecular Relations in Information Transmission and Expression
BSD - Biodegradative Strain Database
HMDB
HMDB - The Human Metabolome Database
KEGG - Kyoto Encyclopedia of Genes and Genomes
Klotho
LIGAND
MedicCyc
MetaCrop
MetaCyc
Metagrowth
MMCD
MODOMICS
NMPDR - National Microbial Pathogen Data Resource
Pathguide
PMAP
PUMA2
SYSTOMONAS
UM-BBD
Protein-protein interactions
3D-Interologs
AffinDB
aMAZE
Argonaute
AtPID
Bacteriome.org
Binding MOAD
BioCarta
BioGRID
CellCircuits
ConsensusPathDB
CORUM
CutDB
Cyclonet
DDIB
DIMA
DIP - Database of Interacting Proteins
Dockground
DOMINE
DOMINO
DRC - Database of Ribosomal Crosslinks
DroID - Drosophila Interactions Database
Dynamic Proteomics
EciD
EndoNet
GeneNet
GLIDA
Hedgehog signalling
Het-PDB Navi
HotSprint
hp-DPI
HPID - Human Protein Interaction database
I2D - Interologous Interaction Database
IMOTdb
IntAct
Inter-Chain Beta-Sheets
InterDom
KDBI
LigAsite
MHC-Peptide Interaction Database
MiMI
MiMI - Michigan Molecular Interactions
MINT
MiST - Microbial Signal Transduction database
Mpact
NetworKIN
NPInter
PANTHER
Pathguide
PathoPlant®
PDZBase
PepCyber:P~Pep
PIG - Pathogen Interaction Gateway
PINdb
PINT
PIPs
POINT
PRODORIC
ProNIT
PROTCOM
Protein kinase resource
Protein-protein interfaces
PRRDB
PSIbase
pSTIING
Reactome
ROSPath
SCOPPI
SENTRA
SMART
STCDB - Signal Transduction Classification Database
STITCH
The Cell Cycle DB
TRANSPATH®
UniHI
VirHostNet
VirusMINT
Wnt Database
Signalling pathways
NetworKIN
PepCyber:P~Pep
PhosPhAt
PID
PRRDB
UCSD-Nature Signaling Gateway Molecule Pages
Human and other Vertebrate Genomes
IUPHAR-DB
Model organisms, comparative genomics
ABA - Ascidian Body Atlas
ACeDB
AgBase
Animal Genome Size Database
AnimalQTLdb
ArkDB
BodyMap
BodyMap-Xs
CCDS
ChickVD
CleanEST
CORG - A database for COmparative Regulatory Genomics
Cre Transgenic Database
DBTGR
diArk
Edinburgh Mouse (EMAP) Atlas
EGO - Eukaryotic Gene Orthologs
Ensembl
Ensembl Genomes
Entrez Gene
euGenes
EuroPhenome
EVOG
ExDom
FREP
GALA
Gallus Gbrowse
GEISHA
GeneNest
GeneSpeed
GXD - Mouse Gene Expression Database
HomoloGene
Homophila
KOG - Eukaryotic Orthologous Groups of proteins
MamPol
MFunGD
MGD - Mouse Genome Database
Mouse Phenome Database
Mouse SAGE
Mouse Transposon Insertion Database
Mouse Tumor Biology Database
MUGEN Mouse Database
Narcisse
Non-Human Genome Segmental Duplication Database
OMIA - Online Mendelian Inheritance in Animals
OPTIC
OrthoDB
PathBase
PBmice
PEDE - Pig Expression Data Explorer
PhylomeDB
PhyloPat
PigGIS
Pseudofam
Rat Genome Database
RatMap
RTCGD - Retroviral Tagged Cancer Gene Database
SNPSTR
SpBase
SPEED
TAED - The Adaptive Evolution Database
TreeFam
UniTrap
UTGB/medaka
VEGA
X:MAP
XenBase
Xpro
ZFIN
Human genome databases, maps and viewers
Cancer Chromosomes
ENCODE Whole-Genome Data in the UCSC Genome Browser
Ensembl
GeneAnnot
GeneCards
GeneLoc
HOWDY
Human BAC Ends Database
Human Genome Segmental Duplication Database
IXDB
QTL Matchmaker
The Chromosome 7 Annotation Project
TRBase
UCSC Genome Browser
UniSTS
X:MAP
Human ORFs
ASDB - Alternative Splicing Database
CCDS
ENCODE Whole-Genome Data in the UCSC Genome Browser
EROP-Moscow
Evola
FANTOM
FLJ-DB
GeneAnnot
GeneSpeed
H-InvDB
HGPD
Hoppsigen
HPRD - Human Protein Reference Database
HS3D - Homo Sapiens Splice Sites Dataset
HUGE - Human Unidentified Gene-Encoded large proteins
Human Proteinpedia
IPI - International Protein Index
LIFEdb
Mammalian Gene Collection
NetAffx
ORFDB
PlasmID
PReMod
SYSTERS
TIGR Gene Indices
trome, trEST and trGEN
UniGene
VEGA
Human Genes and Diseases
Protein Mutant Database
General human genetics databases
BodyParts3D
Comparative Toxicogenomics Database
DG-CST
GenAtlas
GeneCards
Genetics Home Reference
HAGR - Human Ageing Genomic Resources
HCAD - Human Chromosome Aberration Database
HERVd - Human Endogenous Retrovirus database
HGNC Database
Human PAML Browser
MSY Breakpoint Mapper
MutDB
OMIM - Online Mendelian Inheritance in Man
SNP2NMD
General polymorphism databases
ALFRED
CTGA
Cypriot national mutation database
D-HaploDB
Database of Genomic Variants
dbQSNP
dbRIP
dbSNP
F-SNP
FINDbase
HapMap Project
HGVbase
HGVS Databases
HuRef
HvrBase++
IPD - Immuno Polymorphism Database
JSNP
OMIM - Online Mendelian Inheritance in Man
PharmGKB
PhenomicDB
PolyDoms
Polymorphix
rSNP Guide
SNAP
SNP2NMD
SNP@Ethnos
SNPeffect
SNPlogic
TopoSNP
TPMD - Taiwan polymorphic microsatellite marker database
VarySysDB
YH database
Cancer gene databases
Atlas of Genetics and Cytogenetics in Oncology and Haematology
Cancer Chromosomes
CancerGenes
CanGEM
CGED - Cancer Gene Expression Database
ChimerDB
COSMIC - Catalogue Of Somatic Mutations In Cancer
CTDatabase
Database of Germline p53 Mutations
DDOC
EHCO
HPTAA
Human p53, human hprt, rodent lacI and rodent lacZ databases
IARC TP53 Database
ITTACA
MethyCancer
MoKCa
Mouse Tumor Biology Database
OncoDB.HCC
PubMeth
RTCGD - Retroviral Tagged Cancer Gene Database
SNP500Cancer
SV40 Large T-Antigen Mutant Database
Tumor Associated Gene database
Tumor Gene Family Databases (TGDBs)
Gene-, system- or disease-specific databases
ALPSbase
AlzGene
Androgen Receptor Gene Mutations Database
Atlas of Genetics and Cytogenetics in Oncology and Haematology
AutDB
BGED - Brain Gene Expression Database
BTKbase
CarpeDB
CASRDB
Collagen Mutation Database
Cytokine Gene Polymorphisms
dbLEP
DNAreplication.net
EICO DB - Expression-based Imprint Candidate Organiser
EndoNet
EPConDB
EpoDB - Erythropoiesis Database
ERGDB - Estrogen Responsive Genes Database
ERGR
EyeSite
FUNPEP
G2Cdb
GOLD.db - Genomics Of Lipid-associated Disorders
HaemB
HbVar
HDBase
HemBase
HemoPDB - Hematopoietic Promoter Database
HORDE - Human Olfactory Receptor Data Exploratorium
HOX-PRO
HPMR - Human Plasma Membrane Receptome
Human PAX2 Allelic Variant Database
Human PAX6 Allelic Variant Database
IL2Rgbase
Imprinted Gene Catalogue
INFEVERS
Interferome
InterFil
KBERG
KinMutBase
Lowe Syndrome Mutation Database
MDPD
NCL Resource
NEIBank
PAHdb
PGDB
PHEXdb
Prostate Expression Database
PTCH1 Mutation Database
RAPID
RB1 Gene Mutation Database
SCAdb
SynDB
T1DBase - Type 1 Diabetes Database
The Autism Chromosome Rearrangement Database
The Lafora Database
Microarray Data and other Gene Expression Databases
4DXpress
5'SAGE
Drosophila microarray centre
ABA - Ascidian Body Atlas
ArrayExpress
Axeldb
BarleyBase
BGED - Brain Gene Expression Database
BloodExpress
BodyMap
BodyMap-Xs
CAGE
CATMA - Complete Arabidopsis Transcriptome MicroArray
CEBS
CGED - Cancer Gene Expression Database
CleanEx
CycleBase
dbERGEII
Edinburgh Mouse (EMAP) Atlas
EMAGE
EPConDB
EpoDB - Erythropoiesis Database
FLIGHT
GEISHA
Gene Aging Nexus
Gene Expression in Tooth Database
GeneNote
GenePaint
GeneTide
GeneTrap
GENSAT
GEO - Gene Expression Omnibus
GermOnline
GermSAGE
GPX-Macrophage
GXA
GXD - Mouse Gene Expression Database
HemBase
HemoPDB - Hematopoietic Promoter Database
HPMR - Human Plasma Membrane Receptome
HugeIndex - Human Gene Expression Index
Interferon Stimulated Gene Database
International Gene Trap Consortium Database
ITTACA
Kidney Development Database
LOLA
M3D
MAGEST
MAMEP - Molecular Anatomy of the Mouse Embryo Project
MEPD: A Medaka gene expression pattern database
Mouse SAGE
NASCarrays
NetAffx
OncoMine
PEPR - Public Expression Profiling Resource
Prostate Expression Database
RefExA
rOGED
SAGEmap
Sebida
SIEGE
SOURCE
Stanford Microarray Database
TMAD
TmaDB
TRANSFAC®
TRIPLES
yMGV - Yeast microarray global viewer
Proteomics Resources
2D-PAGE
AAindex
Biodefense Proteomics Resource Center
BIOZON
CutDB
dbLEP
dbPTM
DynaProt 2D
GELBANK
MAPU
Open Proteomics Database
PEP: Predictions for Entire Proteomes
PepSeeker
PeptideAtlas
PlantMarkers
PRIDE
RESID
SWISS-2DPAGE
Sys-BodyFluid
SysPIMP
Other Molecular Biology Databases
BioModels
CycleBase
Déjà vu
DNASU Plasmid Repository
HyperCLDB
MetaRouter
PubMed
ReplicationDomain
StrainInfo.net Bioportal
The Cell Cycle DB
University of Pittsburgh Bioinformatics Resources Collection
WormBook
Drugs and drug design
APD - Antimicrobial Peptide Database
BACTIBASE
BioHealthBase
BSD - Biodegradative Strain Database
CEBS
DART - Drug Adverse Reaction Targets
Defensins Knowledgebase
DrugBank
GLIDA
HIV Drug Resistance Database
HIV Molecular Immunology Database
IUPHAR-RD
Peptaibol
PharmGED
PharmGKB
Scorpion
STITCH
SuperDrug
SuperNatural
SuperTarget and Matador
TTD - Therapeutic Target Database
VIOLIN
Molecular probes and primers
AOBase
IMGT/PRIMER-DB
MPDB - Molecular Probe Database
OligoArrayDb
Primer Studio
probeBase
QPPD - Quantitative PCR Primer Database
qPrimerDepot
RTPrimerDB
VirOligo
Organelle databases
Chloroplast Genome Database
FUGOID
GOBASE
Organelle DB
Organelle genomes
PeroxisomeDB
Plant Organelles Database
PLprot
Mitochondrial genes and proteins
HMPD
HmtDB - Human Mitochondrial DataBase
Human MtDB
HvrBase++
MamMiBase
Mitochondriome
MitoDat
MitoDrome
MITOMAP
Mitome
MITOP2
MitoProteome
MitoRes
MPIM - Mitochondrial Protein Import Machinery
OGRe - Organellar Genome Retrieval
PLMItRNA
YDPM - Yeast Deletion Project
YMPD
Plant databases
Chloroplast Genome Database
General plant databases
AgBase
autoSNPdb
BarleyBase
Cereal Small RNA Database
CR-EST - Crop ESTs
DRASTIC
FLAGdb++
GénoPlante-Info
GabiPD
GeneFarm
GrainGenes
Gramene
MetaCrop
MIPSPlantsDB
MPIM - Mitochondrial Protein Import Machinery
P3DB
PathoPlant®
PhytAMP
Phytome
PHYTOPROT
PLACE
Plant DNA C-values database
Plant Genome Central
Plant MPSS
Plant Ontology database
Plant snoRNA DB
Plant Stress-Responsive Gene Catalog
PLANT-PIs
PlantCARE
PlantGDB
PlantProm
PlantsP/PlantsT
PlantTFDB
PlantTribes
POGs/PlantRBP
PPDB: Plant Promoter Database
PPDB: Plant Proteomics Database
SALAD
TAED - The Adaptive Evolution Database
TIGR plant repeat database
TIGR Plant Transcript Assembly database
TropGENE DB
UK CropNet
Arabidopsis thaliana
AGNS - Arabidopsis GeneNet supplementary
AGRIS - Arabidopsis Gene Regulatory Information Server
Arabidopsis Hormone Database
Arabidopsis Mitochondrial Protein Database
Arabidopsis MPSS
Arabidopsis Nucleolar Protein Database
ARAMEMNON
ARTADEdb
ASRP - Arabidopsis Small RNA Project
AtGDB
AthaMap
AtPID
ATTED-II
CATdb
CATMA - Complete Arabidopsis Transcriptome MicroArray
DATF
GABI-Kat
GreenPhylDB
MAtDB
NASCarrays
PhosPhAt
PlantQTL-GE
PLprot
RARGE - RIKEN Arabidopsis Genome Encyclopedia
SeedGenes
SUBA
The Arabidopsis Information Resource (TAIR)
Rice
Oryza Tag Line
BGI-RISe - Beijing Genomics Institute Rice Information System
DRTF
GreenPhylDB
INE
IRIS - International Rice Information System
MOsDB
OryGenesDB
Oryzabase
PlantQTL-GE
RAP-DB
RetrOryza
Rice Annotation Database
Rice Gene Thresher
Rice Mutant Database
Rice Pipeline
Rice Proteome Database
RiceGAAS
Other plants
Brassica BASC
Diatom EST Database
ForestTreeDB
Genome Database for Rosaceae
Legume Information System
MaizeGDB
MedicCyc
MtDB - Medicago trunculata Database
NRESTdb
PANZEA
PoMaMo - Potato Maps and More
SGMD
Shanghai Rapeseed Database
SoyBase
SoyGD
TED - Tomato Expression Database
TIGR Maize database
TomatEST DB
Immunological databases
ALPSbase
AntiJen
BCIpep
dbMHC
Epitome
FIMM
GPX-Macrophage
HaptenDB
HPTAA
IL2Rgbase
IMGT
IMGT-GENE-DB
IMGT/HLA
IMGT/LIGM-DB
Interferon Stimulated Gene Database
IPD-ESTDAB
IPD-HPA - Human Platelet Antigens
IPD-KIR - Killer-cell Immunoglobulin-like Receptors
IPD-MHC
MHC-Peptide Interaction Database
MHCBN
MHCPEP
MUGEN Mouse Database
SuperHapten
The Immune Epitope Database (IEDB)
TmaDB
VBASE2

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