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
APASdb - Alternative PolyAdenylation Sites Database China 4unstable0.84
ChiTaRS - Chimeric Transcripts and RNA-Sequencing data Israel 48alive9.60
COXPRESdb - Coexpression Database Japan 230alive23.00
EPD - Eukaryotic Promoter Database Switzerland 32unstable9.49
TFClass - Classification of Human Transcription Factors and Mouse Orthologs Germany 48unstable6.82
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation United States 363alive40.33
RNAcentral United Kingdom 31alive10.13
tRFdb - Transfer RNA related Fragments Database United States 4alive1.31
miRDB - miRNA target prediction and functional annotations database United States 465alive46.50
DIANA-TarBase - DIANA-TarBase Greece 1513alive126.08
DoRiNA - Database of RNA Interactions in Post-transcriptional Regulation Germany 115unstable16.87
lncRNAdb Australia 351alive49.64
lncRNASNP China 17alive5.44
LncRNA2Target - LncRNA-target association database China 12unstable1.28
InParanoid - ortholog groups with inparalogs Sweden 1253alive95.42
TopFIND - Termini oriented protein Function Inferred Database Canada 98alive14.00
MatrixDB - The extracellular matrix interaction database France 4alive1.32
RaftProt - Mammalian Lipid Raft Proteome Database Australia 0alive0.00
RCSB PDB - RCSB Protein Data Bank United States 853unstable77.99
SASBDB - Small Angle Scattering Biological Data Bank Germany 0alive0.00
Genome3D - Annotating Genomes with Structures United Kingdom 42unstable4.99
IMGT - Knowledge resource specialized in the immunoglobulins or antibodies France 22alive3.63
dbSNO - Database for Cysteine S-Nitrosylation Taiwan 52alive8.41
PhosphoSitePlus United States 653alive108.83
MGD - Mouse Genome Database United States 2658alive126.57
DBTMEE - Database of Transcriptome in Mouse Early Embryos Japan 2alive0.67
MTB - Mouse Tumor Biology System United States 105alive6.18
CCGD - Candidate Cancer Gene Database United States 8alive2.67
DAA - Digital Ageing Atlas United Kingdom 9alive3.00
Organ system heterogeneity DB - A Database for the Visualization of Phenotypes at the Organ System Level Germany 0alive0.00
ImmuCo - a database of gene Co-expression and Correlation in Immune cells China 4unstable1.17
MOPED - Multi-Omics Profiling Expression Database United States 5dead0.03
NGSmethDB - High-quality Methylation Maps Spain 52unstable5.20
miRBase - microRNA dababase United Kingdom 11326alive792.82
miRTarBase - miRNA Target Database Taiwan 899alive128.43
PolymiRTS - Polymorphism in microRNAs and their TargetSites United States 264alive23.76
NONCODE - Noncoding RNAs China 637unstable39.69
NPInter - ncRNA Interaction Database China 119unstable8.63
RADAR - Rigorously Annotated Database of A-to-I RNA editing United States 52alive12.87
JASPAR Canada 2924alive202.59
TFBSshape - DNA shape features of transcription factor binding sites United States 39alive9.75
UniHI - Unified Human Interactome Portugal 194alive17.64
CR Cistrome - Chromatin Regulator Cistrome China 6unstable1.26
Reactome - A Curated Pathway Database United States 615unstable115.31
IMPC - International Mouse Phenotyping Consortium United Kingdom 44alive10.89
GXD - The mouse Gene Expression Database United States 479alive22.81
MPD - Mouse Phenome Database United States 201unstable12.24
EMAGE - Mouse Embryo Spatial Gene Expression Database United Kingdom 234alive18.92
GeneProf - GeneProf United Kingdom 44unstable6.16
CCDS - Consensus Coding Sequence United States 394unstable9.63
Manteia France 18alive4.50
The Gene Expression Barcode United States 15alive3.71
CellFinder Germany 5alive1.25
SAbDab - The Structural Antibody Database United Kingdom 23unstable5.12
MitoBreak - The mitochondrial DNA breakpoints database Portugal 4alive0.98
ENCODE - Encyclopedia of DNA Elements United States 2053unstable32.26
Non-B DB - A Database for Integrated Annotations and Analysis of non-B DNA Forming Motifs United States 68dead0.00
APPRIS - Annotating Principal Splice Isoforms Spain 39alive7.80
ChIPBase China 199unstable25.07
CTCFBSDB - CTCF Binding Sites and Genome Organization Database United States 118alive11.68
HOCOMOCO - Homo Sapiens Comprehensive Model Collection Russian Federation 62alive12.40
SwissRegulon - A Database of Genome-wide Annotations of Regulatory Sites Switzerland 118unstable5.79
NCBI Epigenomics - NCBI Epigenomics United States 51unstable1.68
DIANA-LncBase - Database on miRNA-lncRNA interactions Greece 98unstable17.25
Darned - DAtabase of RNa EDiting Ireland 128alive15.84
TOPPR - The Online Protein Processing Resource Belgium 9unstable1.37
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161unstable19.32
H2DB - Heritability Database Annotating with Trait-Associated Genomic Loci Japan 1unstable0.19
dbVar - Database of Genomic Structural Variation United States 41unstable3.20
TSGene - tumor suppressor gene database United States 89unstable3.56
Allen Brain Atlas United States 67alive13.40
CircaDB - Circadian Database United States 61unstable5.12
HAGR - Human Ageing Genomic Resources United Kingdom 595alive45.77
HemaExplorer Denmark 49unstable7.76
INTERFEROME Australia 224alive24.14
SpermatogenesisOnline - Annotation of Genes/Proteins Involved in Spermatogenesis China 7dead0.00
InnateDB Canada 339unstable29.15
MAPPER2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation United States 116unstable6.34
MMMDB - Mouse Multiple tissue Metabolome DataBase Japan 17alive2.83
IntAct United Kingdom 499unstable60.71
PINA - Protein Interaction Network Analysis Australia 281unstable23.42
OGEE - Online GEne Essentiality database China 77alive12.83
GeneWeaver - GeneWeaver United States 54alive9.00
PrimerBank United States 1063unstable63.78
DNAtraffic - DNAtraffic Poland 3unstable0.38
GONUTS - Gene Ontology Normal Usage Tracking System United States 13unstable1.11
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.29
AREsite - AU-rich Elements Site Austria 110alive15.56
mESAdb - microRNA sequence and expression database Turkey 18alive2.57
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable3.91
PHOSIDA - phosphorylation site database Germany 567unstable47.94
IsoBase - IsoRank PPI Network Alignment Based Ortholog Database United States 44alive6.29
RBPDB - The Database of RNA-binding Protein Specificities Canada 133alive19.00
RNA helicase database United States 30unstable3.77
SCLD - Stem Cell Lineage Database United States 4unstable0.05
KaPPA-View4 - Kazusa Plant Pathway Viewer Japan 36alive5.14
HitPredict Japan 57alive8.14
KUPS - University of Kansas Proteomics Service United States 21unstable0.39
IKMC - The International Knockout Mouse Consortium United States 62unstable2.92
FANTOM - Functional and taxonomic analysis of metagenomes Japan 144alive8.91
Pigment_Cell United States 3unstable0.14
EuroDia - EuroDia MicroArray Database Switzerland 9dead0.00
MRB - Mouse Resource Browser Greece 3alive0.38
CGDSNPdb - Center for Genome Dynamics Single Nucleotide Polymorphism Database United States 7dead0.00
GermOnline - GermOnline France 63unstable4.05
GETPrime - Gene and Transcript-specific Primer Database Switzerland 28unstable3.80
CreZOO - CreZOO Greece 4unstable0.27
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.12
BGDB - Bivalent Genes Database China 4unstable0.04
ESCAPE - Embryonic Stem Cell Atlas from Pluripotency Evidence United States 23alive4.60
CARLSBAD United States 5alive0.98
PhenoDigm - PHENOtype comparisons for DIsease and Gene Models United Kingdom 44unstable8.10
hLGDB - The Human lysosome Gene Database Italy 6alive1.19
YY1TargetDB - Yin Yang 1 Target loci Database Hong Kong SAR China 3alive0.60
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable1.01
Nencki Genomics Database - Ensembl Funcgen Enhanced With Intersections, User Data and Genome-wide TFBS Motifs. Poland 5unstable0.93
GoSynthetic - Synthetic Biology Workbench Germany 2alive0.40
miRBase Tracker - miRBase Tracker Belgium 14unstable3.26
Mouse IDGenes - Gene interactions in the developing mouse brain Germany 1alive0.25
APADB Germany 8alive1.98
miRror-Suite - A dual view on sets of microRNAs and their targets Israel 33alive4.08
EpimiR - Database of Curated Mutual Regulation Between epigenetic Modifications and miRNAs China 8unstable1.44
miRIAD - Intragenic MicroRNA Database Germany 4unstable0.47
miRGate - miRGate Spain 3unstable0.91
CBN - Causal biological network database Switzerland 7alive2.24
MIsoMine - A data portal of expression,function and network of splice isoforms in the mouse United States 3alive0.99
3DGD - 3D Genome Database China 6unstable0.76
ConsensusPathDB Germany 368unstable26.99
NeuroPedia - Neuropeptide Database United States 15alive2.08
PaGenBase - Pattern Gene Database China 8unstable1.47
PEpiD - Prostate Epigenetic Database China 5unstable0.79
SyStemCell China 6unstable0.65
C-It Germany 11alive1.36
TassDB2 - TAndem Splice Site DataBase Germany 45unstable3.80
TiSGeD - Tissue-Specific Genes Database China 64unstable7.44
CIG-DB - Cancer-related Immunological Gene Database Japan 3unstable0.14
MPID-T2 - MHC-Peptide Interaction Database-TR version 2 Australia 8unstable0.72
CircuitsDB Italy 59unstable6.93
ExportAid - Database of RNA elements regulating nuclear RNA export in mammals Italy 1alive0.33
SDOP-DB - A comparative standardised-protocol database Japan 3alive0.38
dbGSH - databaseof cysteine S-glutathionylation (GSH) sites Taiwan 25alive6.19
GPCR-RD - A Database For Experimental Restaints Of GPCRs United States 38alive4.75
DetoxiProt - An integrated database of detoxification proteins China 3unstable0.30
hmChIP United States 28alive4.00
CLIPdb China 0alive0.00
INstruct United States 27alive5.35
IRView - Database and viewer of interacting regions (IRs) in protein sequences Japan 1alive0.17
Hoppsigen - Homologous Processed Pseudogenes database France 44unstable0.41
ECgene - ECgene Korea Rep. 167unstable7.19
TRED - Transcriptional Regulatory Element Database United States 155alive11.57
PolyA_DB United States 83alive6.38
RNAdb Australia 290unstable12.05
SPD - Secreted Protein Database China 119unstable4.58
GenDiS - Genomic Distribution of Protein Structural Domain Superfamilies India 16alive1.23
CORG - Comparative Regulatory Genomics Germany 84dead0.00
GeneNet - The GeneNet system Russian Federation 68alive5.18
DED - Database of Evolutionary Distances United States 6dead0.00
UCSC Proteome Browser - UCSC Proteome Browser United States 51alive3.88
GALA - Genome ALignments and Annotations United States 84alive5.60
dbERGE - the database of Experimental Results on Gene Expression United States 18alive1.38
deepBase - deepBase China 102unstable3.70
DG-CST - Disease Gene Conserved Sequence Tags Database Italy 17alive1.29
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive2.92
EMMA - European Mouse Mutant Archive United Kingdom 34alive4.25
EuroPhenome - EuroPhenome United Kingdom 73unstable6.11
MouseBook - An Integrated Portal of Mouse Resources United Kingdom 9unstable0.76
MouseIndelDB - Mouse Indel Polymorphism Database United States 13unstable0.98
HRTBLDb - Hormone Receptors Target Binding Loci Database United States 9dead0.00
VBASE2 - VBASE2 Germany 104alive8.00
The imprinted gene and parent-of-origin effect database New Zealand 551unstable21.49
Transterm New Zealand 108alive6.55
HOLLYWOOD United States 71alive5.86
ABS - database of Annotated regulatory Binding Sites from orthologous promoters Spain 68alive5.67
cisRED - cisRED Canada 112unstable6.91
ARED Saudi Arabia 928unstable39.85
Argonaute Germany 88alive7.33
GRSDB - ‘G’-Rich Sequences DataBase United States 80alive6.47
miRNAMap - A database of experimentally verified microRNAs and miRNA target genes Taiwan 359alive29.32
RNAi Codex United States 48alive4.00
LOCATE - subcellular localization database Australia 87alive7.25
UCbase & miRfunc - Ultraconserved sequences data and miRNA function United States 58dead0.00
miROrtho - The catalogue of animal microRNA genes Switzerland 55alive6.11
NRED - Noncoding RNA Expression Database Australia 152alive16.89
Degradome - The Degradome database Spain 107dead0.00
SysZNF - the C2H2 zinc finger gene database Germany 31unstable0.65
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable140.83
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.64
PIG - Pathogen Interaction Gateway United States 55unstable1.34
CleanEST Korea Rep. 14alive1.54
EVOG - Evolution Visualizer for Overlapping Genes Korea Rep. 12alive1.33
ExDom - ExDom United States 10unstable0.26
AutDB - Autism Spectrum Disorders database United States 121unstable12.10
ERGR - ethanol-related gene resource United States 32dead0.00
BloodExpress United Kingdom 33alive3.63
GermSAGE - SAGE database for transcript discovery on male germ cell development United States 16unstable0.62
microTranspoGene - The influence of Transposed Elements (TEs) on the biogenesis of microRNAs Israel 56alive5.54
TranspoGene - TranspoGene Israel 56alive5.54
microRNA.org - microRNA.org-Targets and Expression United States 1199unstable107.91
4DXpress - Expression Database in Four Dimensions Germany 36dead0.00
PBmice - PB Mutagenesis Information CEnter China 34dead0.00
EMPReSS - European Mouse Phenotyping Resource of Standardised Screens United Kingdom 64unstable4.29
piRNABank - A web resource on classified and clustered Piwi-interacting RNAs India 111unstable10.32
Vir-Mir - The viral miRNA prediction database Taiwan 60alive5.88
Greglist - Database of G-quadruplex Regulated Genes China 43unstable2.75
QuadBase - QuadBase India 71unstable6.46
PReMod - Predicted Regulatory Modules Canada 94alive8.55
SNPSTR - microsatellite marker and tightly linked SNPs United Kingdom 31alive2.73
GenomeTrafac - GenomeTrafac United States 25alive2.27
MAPU - Max-Planck Unified proteome database Germany 53alive4.72
GAN - Gene Aging Nexus United States 38unstable1.17
GeneSpeed - GeneSpeed database United States 10dead0.00
eSLDB - eSLDB Italy 45alive4.09
MfunGD - MIPS Mouse Functional Genome Database Germany 14unstable0.43
QTL MatchMaker United States 5unstable0.32
CAGE - Cap-analysis gene expression Japan 76alive6.33
IGTC - International Gene Trap Consortium United States 120unstable8.00
MitoP2 - An integrative tool for the analysis of the mitochondrial proteome Germany 156dead0.00
GenBank - GenBank United States 46415unstable548.54
SBR-Blood - Systems Biology Repository United States 0unstable0.00
DIANA-miRGen - DIANA-miRGen Greece 303unstable25.34
SORFS.ORG Belgium 2alive0.98
piRNA cluster db - piRNA cluster database Germany 29alive4.74
iGNM - Gaussian Network Model Database United States 116alive8.92
SEA - Super-Enhancer Archive China 1alive0.50
miRSponge - Experimentally validated miRNA Sponges database China 1unstable0.32
RegNetwork - Regulatory Network Repository United States 0alive0.00
eHistology - eHistology United Kingdom 3alive0.97
NeuroTransDB - Highly Curated and Structured Transcriptomic Metadata for Neurodegenerative Diseases Germany 1unstable0.06
MouseNet - Probabilistic Functional Gene Network for Laboratory Mouse,Mus Musculus Korea Rep. 0unstable0.00
DMDD - Deciphering the Mechanisms of Developmental Disorders United Kingdom 13unstable0.65
dbSUPER - a database of super-enhancers in mouse and human genome China 2unstable0.93
SynLethDB Singapore 1unstable0.47
IID - Integrated interactions database Canada 1alive0.50
BloodSpot Denmark 0alive0.00
dbMAE - The database of autosomal monoallelic expression United States 1alive0.50
KLIFS Netherlands 2alive0.99
RMBase - RNA Modification Base China 2unstable0.67
Metabolomics Workbench United States 0alive0.00
MitoCarta - An Inventory of Mammalian Mitochondrial Genes United States 2unstable0.56
piRNAQuest - searching the piRNAome for silencers India 4alive1.00
MTD - mammalian transcriptomic database China 0alive0.00
GTRD - Gene Transcription Regulation Database Russian Federation 0alive0.00
LNCediting United States 0alive0.00
MethSMRT China 0unstable0.00
miRPathDB - miRNA Pathway Dictionary Database Germany 1dead0.00
POSTAR - POST-trAnscriptional Regulation China 1unstable0.94
R-loopDB Singapore 0alive0.00
TFBSbank United Kingdom 0unstable0.00
WERAM - Writers, Erasers and Readers of Acetylation & Methylation China 1alive1.00
COEXPEDIA Korea Rep. 0alive0.00
Cistrome DB - Cistrome Data Browser China 0alive0.00
KERIS - The kaleidoscope of gene responses to inflammation among species United States 0alive0.00
SinEx DB - SinEx DATABASE Chile 0alive0.00
IRNdb - Database of immunologically relevant non-coding RNAs New Zealand -unstable-
CCSI - Chromatin–Chromatin Spatial Interaction China 0unstable0.00
Wikidata United States 4dead0.00
Tfcheckpoint - Transcription Factor Checkpoint Norway 8alive1.60
Harmonizome United States 5unstable2.22
RAIN - RNA–protein Association and Interaction Networks Switzerland 3unstable1.26
EMAP - e-Mouse Atlas Project United Kingdom 65alive2.47
EpimiRBase Ireland 4unstable1.82
SSBD - Systems Science of Biological Dynamics database Japan 7alive2.33
LncVar - genetic variation associated with long non-coding genes China 2alive1.98
* Citations derived from Google Scholar.
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