Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
MethBank - Methylation Bank China 6alive2.00
COXPRESdb - Coexpression Database Japan 230alive23.00
TTSMI - triplex target DNA site Mapping and Integration database Singapore 1alive0.33
lncRNAdb Australia 351alive49.64
LncRNA2Target - LncRNA-target association database China 12unstable1.20
DB-AT - Database of Apicomplexa Transcriptomes Germany 2alive0.67
UCSC Genome Browser - University of California, Santa Cruz Genome Browser United States 6429alive424.31
VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens United States 382unstable7.29
MGD - Mouse Genome Database United States 2658alive126.57
NHPRTR - Nonhuman Primate Reference Transcriptome Resource United States 31alive6.14
RGD - Rat Genome Database United States 60unstable16.00
SuperFly Spain 0alive0.00
Xenbase - Xenopus model organism database Canada 214alive21.40
DBTMEE - Database of Transcriptome in Mouse Early Embryos Japan 2alive0.67
BCCTBbp - Breast Cancer Campaign Tissue Bank Bioinformatics Portal United Kingdom 3alive0.97
DAA - Digital Ageing Atlas United Kingdom 9alive3.00
Open TG-GATEs - Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System Japan 17dead0.00
Araport - Arabidopsis Information Portal United States 9unstable0.63
ArrayExpress
United Kingdom 289unstable39.30
CODEX
United Kingdom 13alive4.29
GeneFriends - GeneFriends:RNAseq United Kingdom 31alive5.17
ImmuCo - a database of gene Co-expression and Correlation in Immune cells China 4unstable1.17
Cyclebase - Cell-cycle Database Denmark 105unstable7.03
MOPED - Multi-Omics Profiling Expression Database United States 5dead0.03
miRTarBase - miRNA Target Database Taiwan 899alive128.43
PolymiRTS - Polymorphism in microRNAs and their TargetSites United States 264alive23.76
NONCODE - Noncoding RNAs China 637unstable37.24
DEG - Database of Essential Genes China 573alive40.93
COLOMBOS Belgium 35alive5.00
PortEco - potral for E. coli research United States 13alive3.15
SporeWeb Netherlands 11alive2.75
SubtiWiki - A community resource for the model organism Bacillus subtilis Germany 159alive17.49
MycoCosm - The fungal genomics resource United States 93unstable15.58
SGD - Saccharomyces Genome Database United States 772alive128.67
VEGA - Vertebrate Genome Annotation United Kingdom 368unstable25.19
WormBase - WormBase Canada 2150alive126.47
GXD - The mouse Gene Expression Database United States 479alive22.81
MPD - Mouse Phenome Database United States 201unstable11.51
EMAGE - Mouse Embryo Spatial Gene Expression Database United Kingdom 234alive19.11
GeneProf - GeneProf United Kingdom 44unstable5.72
Manteia France 18alive4.50
Expression Atlas - Expression Atlas United Kingdom 90unstable15.08
GEISHA - Gallus Expression In Situ Hybridization Analysis United States 113alive7.83
The Gene Expression Barcode United States 15alive3.71
PED - Pancreatic Expression Database United Kingdom 75unstable6.00
CellFinder Germany 5alive1.25
DECIPHER - Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. United Kingdom 41unstable2.15
NECTAR - Non-synonymous Enriched Coding muTation ARchive United Kingdom 0alive0.00
FINDbase - Frequency of Inherited Disorders Database Greece 111alive10.09
DriverDB - database for cancer driver gene/mutation Taiwan 18alive4.41
Gramene - A comparative resource for plants United States 79alive19.75
GeneTack database - GeneTack database United States 6unstable0.20
ChIPBase China 199unstable25.87
miRGator - miRGator Korea Rep. 228alive22.12
UUCD - ubiquitin and ubiquitin-like conjugation database China 22alive4.40
SIFTS - Structure Integration with Function, Taxonomy and Sequence
United Kingdom 50alive10.00
DGA - Database of Disease and Gene Annotations China 23unstable3.82
dictyBase - Database for Dictyostelium Discoideum United States 128alive14.08
WDDD - Worm Developmental Dynamics Database Japan 4alive0.79
FlyAtlas - Drosophila gene expression atlas United Kingdom 983alive89.36
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161unstable17.98
WholeCellKB - WholeCellKB United States 16alive3.20
OikoBase - A curated genome expression database of Oikopleura dioica Norway 16alive3.07
ZFIN - Zebrafish Information Network United States 899alive42.38
GTR - National Institutes of Health Genetic Testing Registry United States 33unstable2.44
CellLineNavigator Germany 9alive1.80
TSGene - tumor suppressor gene database United States 89unstable3.38
GEO - Gene Expression Omnibus United States 9384unstable217.01
Allen Brain Atlas United States 67alive13.40
CircaDB - Circadian Database United States 61unstable4.88
INTERFEROME Australia 224alive24.14
METscout - METscout
Germany 2alive0.40
MIPS PlantsDB - Plant Genome and Systems Biology Germany 43alive8.60
TropGeneDB - tropical gene database France 34alive2.38
RiceXPro - Rice Expression Profile Database Japan 189unstable24.03
RiceFREND - Rice Functionally Related Gene Expression Network Database Japan 29unstable5.16
DOR - DDBJ Omics Archive
Japan 35unstable4.72
mirEX - MicroRNA Expression Database Poland 16unstable1.79
ViPR - virus pathogene resourse United States 57alive9.50
BµG@Sbase United Kingdom 5unstable0.25
ProPortal - Prochlorococcus Portal United States 18unstable2.76
VFDB - Virulence Factor Database China 448alive34.46
Nematode - Nematode.net United States 163alive11.64
OGEE - Online GEne Essentiality database China 77alive12.83
dbDEPC - Database of Differentially Expressed Proteins in Human Cancer China 22unstable2.01
NCG - Network of Cancer Genes Italy 51alive8.50
modMine - A Data Warehouse for the modENCODE Project United Kingdom 50unstable7.75
MitoZoa - MitoZoa Italy 66dead0.00
MetaCrop - Metabolic pathways in crop plants Germany 73alive7.23
PlantNATsDB - Plant Natural Antisense Transcripts Database China 23alive3.68
PLEXdb - Plant Expression Database United States 136alive22.44
LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes United States 27alive4.37
MPromDb - Mammalian Promoter Database United States 79dead0.00
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive4.62
mESAdb - microRNA sequence and expression database Turkey 18alive2.57
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable3.68
tRNADB-CE - The tRNA Gene DataBase Curated manually by experts
Japan 69alive7.59
TADB - Toxin-antitoxin Data Base China 94unstable12.49
AmoebaDB - Amoeba Genome Resource United States 35alive4.90
MicrosporidiaDB - Microsporidia Genomics Resource United States 35alive4.90
Full-parasites - Full-parasites Indonesia 13alive1.86
CIPRO - Ciona Intestinalis Protein Database Japan 25alive3.57
cBARBEL - Catfish Genome Database United States 26unstable1.23
FANTOM - Functional and taxonomic analysis of metagenomes Japan 144alive8.91
MitoGenesisDB - Mitochondrial Spatio-Temporal Expression Database France 3alive0.42
GreenPhylDB - GreenPhylDB France 130unstable2.73
TFGD - Tomato Functional Genomics Database United States 46alive6.44
EuroDia - EuroDia MicroArray Database Switzerland 9dead0.00
BrainTrap - Fly Brain Protein Trap Database United Kingdom 14alive1.72
GermOnline - GermOnline France 63unstable4.10
SalmonDB - A Database for salmonids species Chile 14alive1.94
CELLPEDIA Japan 10alive1.43
GETPrime - Gene and Transcript-specific Primer Database Switzerland 28unstable3.56
modENCODE - The model organism Encyclopedia of DNA Elements United States 18alive2.57
The strategies WDK United States 9unstable1.04
TparvaDB - Theileria parva vaccine development Database Kenya 2dead0.00
ParkDB - Parkinson's disease gene expression database United Kingdom 18dead0.00
yApoptosis - yeast apoptosis database Sweden 1alive0.20
ESCAPE - Embryonic Stem Cell Atlas from Pluripotency Evidence United States 23alive4.60
PhenoDigm - PHENOtype comparisons for DIsease and Gene Models United Kingdom 44unstable7.57
curatedOvarianData United States 30unstable3.96
GnpIS - Genetic and Genomic Information System France 9unstable0.41
dbWFA - Database of Wheat Functional Annotation France 2unstable0.09
bc-GenExMiner - Breast Cancer Gene-Expression Miner France 13alive2.60
RGED - Renal Gene Expression Database China 1alive0.25
Mouse IDGenes - Gene interactions in the developing mouse brain Germany 1alive0.25
yStreX - Yeast stress expression database Sweden 2alive0.50
WholeCellSimDB United States 4unstable0.92
MorusDB - the Morus Genome Database China 4unstable0.69
CancerEST United Kingdom 3alive0.75
BioXpress United States 5unstable0.35
LOTUS-DB - Lotus database China 0unstable0.00
MIsoMine - A data portal of expression,function and network of splice isoforms in the mouse United States 3alive0.99
GermlncRNA - Germ Cell Long non-coding RNAs Database Hong Kong SAR China 2alive0.67
GraP - Platform of Functional Genomics Analysis in Gossypium raimondii China 1unstable0.30
RNA-Seq Atlas Germany 74alive12.33
PaGenBase - Pattern Gene Database China 8unstable1.47
Genevar - GENe Expression VARiation United Kingdom 231unstable24.83
VTCdb - ViTis Co-expression DataBase Australia 10unstable1.74
RARGE II - Arabidopsis Genome Encyclopedia Japan 7alive1.73
SNPxGE2 United States 4unstable0.45
MCG - Maize Cell Genomics Database United States 4alive1.33
C-It Germany 11alive1.36
WheatGenome.info - WheatGenome.information Australia 30alive4.95
STPD - salinity tolerant poplar database China 0unstable0.00
TiSGeD - Tissue-Specific Genes Database China 64unstable7.44
MOROKOSHI - MOROKOSHI Sorghum transcriptome database Japan 5alive1.67
Bioclock - The Aedes aegypti Circadian Database United States 2alive0.49
UniVIO - Uniformed Viewer for Integrative Omics Japan 13alive2.57
CoP - Co-expressed biological Processes Japan 51alive6.31
dbCerEx - database of Cervical Cancer Gene Expression China 0dead0.00
SurvExpress Mexico 37unstable5.40
MGEx-Udb - Mammalian Gene Expression Uterus database India 6alive0.96
Liverome - A database of liver cancer-related gene lists Korea Rep. 19alive2.71
NPRD - Nucleosome Positioning Region Database Russian Federation 20alive1.52
TGI - TIGR Gene Index database United States 214alive16.46
ECgene - ECgene Korea Rep. 167unstable6.68
SpliceInfo Taiwan 37alive2.79
PartiGeneDB - A Database of Partial Genomes Canada 12alive0.89
MDS_IES_DB - MDS, IES, and pointer annotations for Oxytricha and Tetrahymena United States 34alive2.56
SilkDB China 293unstable7.89
SilkSatDb India 28alive2.15
GALA - Genome ALignments and Annotations United States 84alive5.60
dbERGE - the database of Experimental Results on Gene Expression United States 18alive1.38
CGED - Cancer Gene Expression data Japan 46dead0.00
GeneTide - Gene Terra Incognita Discovery Endeavor Israel 10dead0.00
H-ANGEL - Human Anatomic Gene Expression Library Japan 24dead0.00
SIEGE - Smoking Induced Epithelial Gene Expression United States 28dead0.00
SMD - Stanford Microarray Database
United States 218alive16.77
BB - BarleyBase United States 101unstable0.39
openSputnik - A database to ESTablish comparative plant genomics Finland 28dead0.00
Patrocles Belgium 114unstable13.11
PLANdbAffy - probe-level annotation database for Affymetrix expression microarrays Russian Federation 28alive3.47
PSI-MR - Protein Structure Initiative Material Repository United States 105alive12.99
Oracle Database 10g
United States 35alive2.69
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable224.25
PRODORIC - PROcariotIC Database Of Gene-Regulation Germany 52unstable5.14
NRED - Noncoding RNA Expression Database Australia 152alive16.89
FlyEx - Fly Expression Databse Russian Federation 83unstable7.10
Nematode.net - A Tool for Navigating Sequences from Parasitic and Free-living Nematodes United States 165alive11.79
CleanEST Korea Rep. 14alive1.49
BloodExpress United Kingdom 33alive3.63
CleanEx
Switzerland 8unstable0.66
GermSAGE - SAGE database for transcript discovery on male germ cell development United States 16unstable0.59
RTPrimerDB - real-time quantitative PCR primers
Belgium 102unstable7.93
ATTED-II Japan 711alive64.64
microRNA.org - microRNA.org-Targets and Expression United States 1199unstable100.72
OTL - Oryza Tag Line Database France 51alive5.10
TAIR - The Arabidopsis Information Resource United States 768unstable43.01
TMAD - The Stanford Tissue Microarray Database
United States 55unstable3.47
M3D - Many Microbe Microarrays Database United States 195alive19.50
4DXpress - Expression Database in Four Dimensions Germany 36dead0.00
CanGEM - Cancer GEnome Mine Finland 35unstable2.20
UTGB - University of Tokyo Genome Browser Medaka Japan 26alive2.60
PBmice - PB Mutagenesis Information CEnter China 34dead0.00
Gallus GBrowse - A Unified Genomic Database for the Chicken United States 14unstable0.15
EndoNet - EndoNet
Germany 24alive1.98
HEG-DB - The highly expressed genes database Spain 271alive23.90
ToxoDB - Toxoplasma gondii database United States 381alive24.89
SGDB - Synthetic Gene Database
United States 26unstable1.02
qPrimerDepot - qPrimerDepot
United States 105unstable5.15
PathoPlant - PathoPlant Germany 33alive2.97
ForestTreeDB - ForestTreeDB Canada 29unstable1.56
TomatEST - Tomato expressed sequence tag Italy 26unstable2.10
GAN - Gene Aging Nexus United States 38unstable1.11
EPConDB - EPConDB United States 15alive1.36
OncoDB.HCC - Oncogenomic Database of Hepatocellular Carcinoma Taiwan 61alive5.49
WormBook - the online review of Caenorhabditis elegans biology United States 51alive4.64
ViTa - ViTa Taiwan 56alive5.04
CryptoDB United States 87alive7.11
PFGD - Phytophthora Functional Genomics Database United States 21alive1.68
BodyMap-Xs
Japan 26dead0.00
CAGE - Cap-analysis gene expression Japan 76alive6.33
PepSeeker - A database of proteome peptide identifications for investigating fragmentation patterns United Kingdom 38dead0.00
TED - Tomato Expression Database United States 68alive5.55
FFGED - Filamentous Fungal Gene Expression Database United States 27alive3.31
MERAV - Metabolic gEne RApid Visualizer United States 0alive0.00
TCGASpliceSeq - TCGASpliceSeq United States 0alive0.00
CRN - Cancer RNA-Seq Nexus Taiwan 0alive0.00
Lynx United States 0alive0.00
IC4R - Information Commons for Rice China 1alive0.50
SBR-Blood - Systems Biology Repository United States 0unstable0.00
EBI - The European Bioinformatics Institute United Kingdom 610unstable17.28
WeGET - Weighted Gene Expression Tool and database Netherlands 0unstable0.00
SEA - Super-Enhancer Archive China 1alive0.50
PlanMine Germany 1alive0.50
GEneSTATION United States 1alive0.48
NCBI - National Center for Biotechnology Information United States 16174unstable323.48
miRNASNP - microRNA-related Single Nucleotide Polymorphisms China 145alive23.44
SHIELD - Shared Harvard Inner Ear Laboratory Database United States 0alive0.00
EpiFactors - EpiFactors Russian Federation 3alive0.99
ccmGDB - Cancer Cell Metabolism Gene DataBase United States 2unstable0.17
BloodSpot Denmark 0alive0.00
dbMAE - The database of autosomal monoallelic expression United States 1alive0.50
Colorectal Cancer Atlas Australia 1alive0.50
CircNet
Taiwan 0unstable0.00
MEPD - Medaka Expression Pattern Database Germany 0alive0.00
Lnc2Cancer China 2unstable0.95
ANISEED France 2unstable0.48
PGSB PlantsDB - Plant Genome and Systems Biology PlantsDB Germany 1alive0.50
dPORE-miRNA - Dragon Database of Polymorphic Regulation of miRNA genes Saudi Arabia 25alive3.43
GSA - Genome Sequence Archive China 4unstable3.80
WikiCell China 8alive1.28
AlzBase - an integrative database for gene dys-regulation in Alzheimer’s disease China 5alive2.50
MTD - mammalian transcriptomic database China 0alive0.00
HRGD - Heterosis Related gene Database China 6unstable0.63
BIG Data Center - BIG Data Center for Life & Health Sciences China 12alive12.00
COEXPEDIA Korea Rep. 0alive0.00
SoyNet Korea Rep. 0unstable0.00
ccNET China 0unstable0.00
SlideBase Denmark 0alive0.00
RSIADB - Rice Sheath Blight Pathogen Genomics Database China 1alive0.50
PepPSy France 0unstable0.00
EMAP - e-Mouse Atlas Project United Kingdom 65alive2.47
RED - Rice Expression Database China 0alive0.00
* Citations derived from Google Scholar.
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