Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
euL1db - European database of L1HS retrotransposon insertions in humans France 2unstable0.61
APASdb - Alternative PolyAdenylation Sites Database China 4unstable0.73
ChiTaRS - Chimeric Transcripts and RNA-Sequencing data Israel 48alive9.60
COXPRESdb - Coexpression Database Japan 230alive23.00
DBTSS - DataBase of Transcriptional Start Sites Japan 767alive47.94
EPD - Eukaryotic Promoter Database Switzerland 32unstable8.32
TFClass - Classification of Human Transcription Factors and Mouse Orthologs Germany 48unstable6.05
Gbshape - Genome Browser Database for DNA Shape Annotations United States 8alive2.67
TTSMI - triplex target DNA site Mapping and Integration database Singapore 1alive0.33
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation United States 363alive40.33
RNAcentral United Kingdom 31unstable9.40
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 115unstable14.95
lncRNAdb Australia 351alive49.64
LNCipedia - A comprehensive compendium of human long non-coding RNAs Belgium 168unstable17.47
lncRNASNP China 17alive5.44
LncRNAWiki - a wiki-based platform for community curation of human lncRNAs China 15unstable4.15
LncRNA2Target - LncRNA-target association database China 12unstable1.12
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 0unstable0.00
RCSB PDB - RCSB Protein Data Bank United States 853unstable69.46
Genome3D - Annotating Genomes with Structures United Kingdom 42alive5.04
Platinum - Protein-ligand affinity change upon mutation United Kingdom 0unstable0.00
IMGT - Knowledge resource specialized in the immunoglobulins or antibodies France 22alive3.63
IPD - Immuno Polymorphism Database United Kingdom 323unstable15.90
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
dbSNO - Database for Cysteine S-Nitrosylation Taiwan 52alive8.41
PhosphoSitePlus United States 653alive108.83
DEPOD - Human DEPhOsphorylation Database Germany 0unstable0.00
HIV-1 Human Interaction Database United States 171unstable5.81
neXtProt - Exploring the universe of human proteins Switzerland 237unstable9.48
AFND - Allele Frequency Net Database United Kingdom 39alive7.80
OMIM - Online Mendelian Inheritance in Man United States 3217unstable32.17
GRASP - Genome-Wide Repository of Associations between SNPs and Phenotypes United States 28unstable2.52
COSMIC - Catalogue of Somatic Mutations in Cancer United Kingdom 4018unstable223.86
The UCSC Cancer Genomics Browser United States 187unstable3.95
arrayMap Switzerland 0unstable0.00
BCCTBbp - Breast Cancer Campaign Tissue Bank Bioinformatics Portal United Kingdom 3alive0.97
CMPD - Cancer Mutant Proteome Database Taiwan 0unstable0.00
Cancer3D United States 10unstable3.13
MethHC - A database of DNA Methylation and gene expression in Human Cancer Taiwan 18alive5.94
YM500 - YM500 Taiwan 45alive8.82
VaDE - VarySysDB Disease Edition Japan 0alive0.00
DAA - Digital Ageing Atlas United Kingdom 9alive3.00
Dr.VIS - Viral integration sites China 14unstable1.17
EpilepsyGene - EpilepsyGene database China 3unstable0.60
ADReCS - Adverse Drug Reaction Classification System China 3unstable0.93
Open TG-GATEs - Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System Japan 17dead0.00
T3DB - The Toxin and Toxin Target Database Canada 73alive9.13
AHTPDB - Database of Antihypertensive Peptides India 7alive2.33
PubAngioGen China 0unstable0.00
GO - Gene Ontology Consortium Switzerland 5117alive301.00
DO - Disease Ontology United States 248alive40.92
HGNC - HUGO Gene Nomenclature Committee United Kingdom 612unstable39.17
GeneFriends - GeneFriends:RNAseq United Kingdom 31alive5.17
ImmuCo - a database of gene Co-expression and Correlation in Immune cells China 4unstable1.13
Cyclebase - Cell-cycle Database Denmark 105unstable6.62
MOPED - Multi-Omics Profiling Expression Database United States 5dead0.03
VCGDB - Virtual Chinese Genome Database China 1alive0.25
NGSmethDB - High-quality Methylation Maps Spain 52unstable5.50
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
starBase - starBase China 491unstable56.82
NONCODE - Noncoding RNAs China 637unstable35.28
NPInter - ncRNA Interaction Database China 119unstable7.64
RADAR - Rigorously Annotated Database of A-to-I RNA editing United States 52alive12.87
JASPAR Canada 2924alive200.50
TFBSshape - DNA shape features of transcription factor binding sites United States 39unstable8.97
BloodChIP Australia 11unstable0.80
DPRP - Database of Phenotype-specific Regulatory Programs Taiwan 0alive0.00
KEGG - Kyoto Encyclopedia of Genes and Genomes Japan 25114alive1321.79
UniCarbKB - UniCarb KnowledgeBase Australia 85alive11.90
Gene3D - Gene3D United Kingdom 194alive19.21
UniHI - Unified Human Interactome Portugal 194alive17.64
GPCRDB - G Protein-coupled Receptor (GPCR) Database Denmark 964alive47.72
Laminin-database Brazil 4unstable0.94
CentrosomeDB Spain 58unstable5.48
Hemolytik - Database of Hemolytic peptides India 13alive3.25
CR Cistrome - Chromatin Regulator Cistrome China 6unstable1.25
Reactome - A Curated Pathway Database United States 615unstable103.01
SMPDB - The Small Molecule Pathway Database Canada 110alive13.48
WormQTLHD - A Web Database for Linking Human Disease to Natural Variation Data in C. elegans. Netherlands 27alive5.40
GeneProf - GeneProf United Kingdom 44unstable5.43
CCDS - Consensus Coding Sequence United States 394unstable8.32
LRG - Locus Reference Genomic United Kingdom 155alive19.38
Manteia France 18alive4.50
AgeFactDB - Ageing Factor Database Germany 8alive2.00
dbPSHP - Database of Positive Selection across Human Populations Hong Kong SAR China 16alive4.00
Selectome - A Database of Positive Selection Switzerland 43unstable3.92
Expression Atlas - Expression Atlas United Kingdom 90unstable14.18
The Gene Expression Barcode United States 15alive3.71
PED - Pancreatic Expression Database United Kingdom 75unstable5.66
CellFinder Germany 5alive1.25
PPD - Plasma Proteome Database India 53unstable12.45
dbGaP - Database of Genotypes and Phenotypes United States 85unstable7.44
ClinVar - variation-phenotype relationships United States 944unstable82.60
DGV - Database of Genomic Variants Canada 233alive58.25
DECIPHER - Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. United Kingdom 41unstable1.95
NECTAR - Non-synonymous Enriched Coding muTation ARchive United Kingdom 0alive0.00
FINDbase - Frequency of Inherited Disorders Database Greece 111alive10.09
InvFEST - Human Polymorphic Inversion DataBase Spain 14alive3.50
rSNPBase - A Database for Curated Regulatory SNPs China 35alive8.75
canSAR United Kingdom 70unstable10.27
DriverDB - database for cancer driver gene/mutation Taiwan 18alive4.41
Progenetix Switzerland 179unstable6.53
HbVar - Human Hemoglobin Variants and Thalassemias United States 510alive36.43
HMDD - Human MicroRNA Disease Database China 61alive14.95
SuperPain Germany 3alive0.75
Transformer Germany 8alive2.00
TTD - Therapeutic target database Singapore 232alive37.89
VIOLIN - Vaccine investigation and online information network United States 20alive5.00
SAbDab - The Structural Antibody Database United Kingdom 23unstable4.54
MitoBreak - The mitochondrial DNA breakpoints database Portugal 4alive0.98
ENCODE - Encyclopedia of DNA Elements United States 2053unstable27.86
SINEBase - A Database and Tools for SINE Analysis Russian Federation 27alive5.35
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
HEXEvent - Human EXon splicing Events database United States 14alive2.72
SpliceAid-F Italy 20dead0.00
Spliceosome Database United States 20alive3.88
Factorbook - Factorbook United States 61unstable2.20
ChIPBase China 199unstable26.67
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 118unstable5.15
NCBI Epigenomics - NCBI Epigenomics United States 51unstable1.46
DIANA-LncBase - Database on miRNA-lncRNA interactions Greece 98unstable17.25
miRGator - miRGator Korea Rep. 228alive22.12
Darned - DAtabase of RNa EDiting Ireland 128alive15.84
MODOMICS - A Database of RNA Modifications Poland 509alive41.99
RNApathwaysDB - RNA Pathways Database Poland 5alive0.99
TOPPR - The Online Protein Processing Resource Belgium 9unstable1.21
ValidNESs - Validated NES-containing proteins, functional NES sites and NES predictions Taiwan 21unstable3.95
EENdb - Database of Engineered EndoNucleases China 35unstable6.58
KIDFamMap - Kinase-inhibitor-disease family map Taiwan 6alive1.20
D2P2 - Database of Disordered Protein Prediction United Kingdom 80alive15.84 - HGNC United Kingdom 785unstable50.24
DGA - Database of Disease and Gene Annotations China 23unstable3.59
HBVdb - Hepatitis B Virus database France 16unstable1.63
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161unstable16.91
CPDB - Consensus Pathway Database Germany 368unstable29.03
HMDB - The Human Metabolome Database Canada 2615alive235.35
PrePPI - A structure-informed database of protein-protein interactions United States 301unstable13.04
SynSysNet - Synaptic Proteins Database Germany 18alive3.60
TissueNet - The Database of Human Tissue Protein-Protein Interactions Israel 53alive10.39
H2DB - Heritability Database Annotating with Trait-Associated Genomic Loci Japan 1unstable0.19
H-InvDB - H-Invitational Database Japan 109alive10.90
Atlas of Genetics and Cytogenetics in Oncology and Haematology - Atlas of Genetics and Cytogenetics in Oncology and Haematology France 1188alive66.00
GTR - National Institutes of Health Genetic Testing Registry United States 33unstable2.31
dbVar - Database of Genomic Structural Variation United States 41unstable2.79
CellLineNavigator Germany 9alive1.80
GDSC - Genomics of Drug Sensitivity in Cancer United Kingdom 114unstable17.78
TP53 mutation database France 30unstable4.98
TSGene - tumor suppressor gene database United States 89unstable3.03
SomamiR United States 27alive5.35
LncRNADisease - Database on lncRNA-disease associations China 267unstable26.17
Allen Brain Atlas United States 67alive13.40
CircaDB - Circadian Database United States 61unstable4.51
GenomeRNAi - A Database for Cell-based and In Vivo RNAi Phenotypes Germany 45alive8.82
HAGR - Human Ageing Genomic Resources United Kingdom 595alive45.77
HemaExplorer Denmark 49alive7.84
INTERFEROME Australia 224alive23.89
SpermatogenesisOnline - Annotation of Genes/Proteins Involved in Spermatogenesis China 7dead0.00
LUCApedia - Last Universal Common Ancestor United States 10unstable1.26
IUPHAR-DB United Kingdom 144alive20.16
G4LDB - G-quadruplex ligands database China 24unstable3.02
IMGT/HLA United Kingdom 370unstable47.36
InnateDB Canada 339unstable29.83
CIL-CCDB - Cell Image Library United States 14alive2.69
SRA - Sequence Read Archive United States -unstable-
MAPPER2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation United States 116unstable5.53
SitEx Russian Federation 5alive0.82
DD - Database of Death Domain Korea Rep. 14alive2.33
Histome - The Histone Infobase India 49unstable7.76
Cube-DB - Cube-DB Singapore 3alive0.49
hiPathDB - human integrated Pathway DB with facile visualization Korea Rep. 24unstable3.64
HotRegion Turkey 23alive3.83
IntAct United Kingdom 499unstable53.23
PINA - Protein Interaction Network Analysis Australia 281unstable24.35
Predictive networks United States 24unstable3.56
OGEE - Online GEne Essentiality database China 77alive12.83
HGPD - Human Gene and Protein Database Japan 36alive4.00
HaploReg United States 457unstable47.22
SNPeffect - Single Nucleotide Variants Belgium 261alive20.08
DPSC-Cancer - Donnelly - Princess Margaret Screening Centre Cancer Database Canada 24alive3.96
dbDEPC - Database of Differentially Expressed Proteins in Human Cancer China 22unstable1.87
IGDB.NSCLC - Integrated Genomic Database of Non-Small Cell Lung Carcinoma Taiwan 10alive1.65
NCG - Network of Cancer Genes Italy 51alive8.50
SCDE - Stem Cell Discovery Engine United States 23alive3.83
UMD-BRCA1/BRCA2 - Universal mutation database-BRCA1/BRCA2 France 23dead0.00
ADHDgene - Database for Attention Deficit Hyperactivity Disorder China 27alive4.45
ALFRED - The ALlele FREquency Database United States 74unstable1.43
AutismKB China 74unstable8.88
BGMUT - Blood Group Antigen Gene Mutation Database United States 43unstable2.51
DiseaseMeth - Human Disease Methylation Database China 56alive8.96
DistiLD - Database of Diseases and Traits in Linkage Disequilibrium Denmark 17alive2.83
GWASdb - GWASdb Hong Kong SAR China 82alive13.67
SpliceDisease China 27dead0.00
GeneSigDB - Gene Signature DataBase United States 123unstable8.30
GeneWeaver - GeneWeaver United States 54unstable8.28
DAMPD - Dragon Antimicrobial Peptide Database South Africa 39unstable3.44
TDR - Tropical Disease Research Argentina 43unstable6.67
OligoGenome - Stanford Human Oligo Genome Project United States 3unstable0.43
PrimerBank United States 1063unstable64.49
HmtDB - Human Mitochondrial DataBase Italy 99unstable4.87
DIGIT - Database of ImmunoGlobulins with Integrated Tools Italy 19alive3.10
DNAtraffic - DNAtraffic Poland 3unstable0.34
MethylomeDB - database containing genome-wide brain DNA methylation profiles United States 33unstable1.87
Gene Wiki - Gene Wiki United States 113unstable2.68
SNPedia United States 67unstable9.05
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.29
KGVDB Korea Rep. 4dead0.02
AREsite - AU-rich Elements Site Austria 110alive15.56
DBASS - Databases of Aberrant 3'-ss and 5'-ss in Human Disease Genes Italy 19alive2.71
TcoF-DB - Dragon database of transcription co-factors and transcription factor interacting proteins Saudi Arabia 36alive4.94
mESAdb - microRNA sequence and expression database Turkey 18alive2.57
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable3.44
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable2.97
PHOSIDA - phosphorylation site database Germany 567unstable42.78
PolyQ - Polyglutamine Australia 18unstable2.03
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 30unstable3.34
SAHG - Structure Atlas of Human Genome Japan 8unstable0.54
IGRhCellID - Integrated Genomic Resources of Human Cell Lines for Identification Taiwan 2alive0.28
SCLD - Stem Cell Lineage Database United States 4unstable0.04
KaPPA-View4 - Kazusa Plant Pathway Viewer Japan 36alive5.14
HitPredict Japan 57alive8.14
KUPS - University of Kansas Proteomics Service United States 21unstable0.33
RegPhos - Regulatory Network in Protein Phosphorylation Taiwan 49alive6.79
REPAIRtoire - A Database of DNA Repair Pathways Poland 24alive3.39
SPIKE - Signaling Pathways Integrated Knowledge Engine Israel 38alive5.43
FANTOM - Functional and taxonomic analysis of metagenomes Japan 144alive8.91
TIARA - Total Integrated Archive of Short-Read and Array database Korea Rep. 15alive2.12
DAnCER - Disease Annotated Chromatin Epigenetics Resource Canada 17unstable2.26
dbCRID - Chromosomal Rearrangements In Diseases United States 23unstable0.46
dbDNV - DNV Database Taiwan 11unstable1.35
IGDD India 13unstable1.50
VnD - Variations and Drugs Korea Rep. 7dead0.00
CancerResource Germany 59alive8.34
CaSNP China 17unstable1.31
CCDB - Cervical Cancer Gene Database India 42alive6.00
DDPC - Dragon Database of Genes associated with Prostate Cancer South Africa 26unstable3.49
CADgene - Coronary Artery Disease Gene Database China 42unstable5.16
T1DBase - type 1 diabetes susceptibility Base United Kingdom 178unstable4.24
Pigment_Cell United States 3unstable0.13
EuroDia - EuroDia MicroArray Database Switzerland 9dead0.00
human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactions Germany 14alive1.73
TRedD - Tandem Repeats Database United States 12unstable0.52
Varietas - Varietas Finland 8dead0.00
GermOnline - GermOnline France 63unstable4.10
GeneCards - GeneCards Israel 900unstable18.45
HyperCAT Norway 20alive2.45
hUbiquitome - ubiquitination cascades in humans China 14dead0.00
CELLPEDIA Japan 10alive1.43
Reactome BioMart - Reactome BioMart United Kingdom 8dead0.00
ICGC - International Cancer Genome Consortium Data Portal Canada 80dead0.00
GETPrime - Gene and Transcript-specific Primer Database Switzerland 28unstable3.32
hERGAPDbase Japan 5unstable0.26
LPS-annotate Canada 8dead0.02
ParkDB - Parkinson's disease gene expression database United Kingdom 18dead0.00
CTD - Comparative Toxicogenomics Database United States 1016alive67.73
dbPTB - Database for Preterm Birth United States 16alive2.67
MEDIC - CTD's MEDIC disease vocabulary United States 54alive9.00
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.24
RefPrimeCouch - A Reference Gene Primer CouchApp Germany 1unstable0.16
HypoxiaDB - Hypoxia regulated proteins database India 3alive0.59
RAvariome - Rheumatoid Arthritis Genetic Variants Database Japan 4alive0.78
HTS-DB - High-Throughput Screening DataBase United Kingdom 0alive0.00
IQdb - IQ genetic database China 8unstable0.43
metabolicMine - metabolicMine United Kingdom 10dead0.00
BGDB - Bivalent Genes Database China 4unstable0.04
lncRNome - long noncoding RNA knowledgebase India 37unstable7.03
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 44unstable7.13
hLGDB - The Human lysosome Gene Database Italy 6alive1.19
Variome - Variome Japan 4unstable0.34
MalaCards - The Human Disease Database Israel 97unstable7.76
curatedOvarianData United States 30unstable3.72
YY1TargetDB - Yin Yang 1 Target loci Database Hong Kong SAR China 3alive0.60
T-HOD - Text-mined Hypertension, Obesity and Diabetes candidate gene database Taiwan 9unstable1.53
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable0.90
PPInterFinder - Protein-Protein Interactions Finder India 17unstable0.20
Nencki Genomics Database - Ensembl Funcgen Enhanced With Intersections, User Data and Genome-wide TFBS Motifs. Poland 5unstable0.82
BBGRE - Brain & Body Genetic Resource Exchange United Kingdom 2dead0.02
T2D@ZJU - Type 2 Diabetes Database at Zhejiang University China 6unstable0.32
CHD@ZJU - Coronary Heart Disease Research Platform China 7unstable0.69
GoSynthetic - Synthetic Biology Workbench Germany 2alive0.40
FSRD - Fungal Stress Response Database Hungary 8alive1.58
pseudoMap Taiwan 10alive2.00
bc-GenExMiner - Breast Cancer Gene-Expression Miner France 13alive2.60
HGV&TB - Database for Human Genes and Genetic Variants associated with Tuberculosis India 0unstable0.00
MelGene - Field Synopsis of Genetic Association Studies in Cutaneous Melanoma Greece 4unstable0.69
CGHub - Cancer Genomics Hub United States 26unstable1.24
RGED - Renal Gene Expression Database China 1alive0.25
RADB - A Database of Rheumatoid Arthritis Related Polymorphisms China 1alive0.25
LiverCancerMarkerRIF Taiwan 2unstable0.39
miRBase Tracker - miRBase Tracker Belgium 14unstable3.29
APADB Germany 8alive1.98
miRror-Suite - A dual view on sets of microRNAs and their targets Israel 33alive4.08
PhenotypeAnnotation Spain 4alive0.97
Osteosarcoma Database - An Osteosarcoma-gene Association Database Germany 4alive0.99
TuberQ Argentina 7unstable1.19
EpimiR - Database of Curated Mutual Regulation Between epigenetic Modifications and miRNAs China 8unstable1.50
ALE-HSA21 - AnaLysis of Expression of HSA21 Italy 5unstable1.15
TSLP signaling pathway map - Thymic stromal lymphopoietin signaling pathway map United States 10unstable2.30
ANIA - ANnotation and Integrated Analysis of the 14-3-3 interactome United Kingdom 6unstable0.28
Kin-Driver Argentina 7unstable1.66
miRIAD - Intragenic MicroRNA Database Germany 4unstable0.53
RetinoGenetics China 5unstable1.17
CancerEST United Kingdom 3alive0.75
HPVdb - Human Papillomavirus T cell Antigen Database United States 11alive2.75
BioXpress United States 5unstable0.33
miRGate - miRGate Spain 3unstable0.87
DisGeNET - DisGeNET Spain 185alive23.13
CBN - Causal biological network database Switzerland 7alive2.24
RNA-Seq Atlas Germany 74alive12.33
3DGD - 3D Genome Database China 6unstable0.67
ConsensusPathDB Germany 368unstable28.62
dbNSFP - database for nonsynonymous SNPs' functional predictions United States 261unstable3.73
NeuroPedia - Neuropeptide Database United States 15alive2.10
NGS catalog - A Database of Next Generation Sequencing Studies in Humans United States 23unstable0.65
PaGenBase - Pattern Gene Database China 8unstable1.46
PEpiD - Prostate Epigenetic Database China 5unstable0.80
KEGGtranslator - KEGGtranslator Germany 69unstable9.36
PhosphoNetworks United States 11alive2.75
KMeyeDB - Keio Mutation eye Databases Japan 2unstable0.22
Genevar - GENe Expression VARiation United Kingdom 231unstable23.39
HIPdb - Database of HIV inhibiting peptides India 19alive3.80
HTRIdb - Human Transcriptional Regulation Interaction Database Brazil 45unstable5.03
SNPxGE2 United States 4unstable0.43
SyStemCell China 6unstable0.58
C-It Germany 11alive1.36
TassDB2 - TAndem Splice Site DataBase Germany 45unstable3.72
microPIR - microRNA-Promoter Interaction Resource Thailand 17alive2.81
seeQTL United States 58unstable7.25
The international dystrophic epidermolysis bullosa patient registry Netherlands 26unstable0.71
The Ruby UCSC API Japan 0unstable0.00
MirSNP - A collection of human SNPs in predicted miRNA target sites. China 67unstable10.50
miRvar - A comprehensive database for genomic variations in microRNAs India 22unstable2.99
TiSGeD - Tissue-Specific Genes Database China 64unstable7.44
RCPedia - a database of retrocopied genes. Brazil 5unstable0.53
CIG-DB - Cancer-related Immunological Gene Database Japan 3unstable0.12
MPID-T2 - MHC-Peptide Interaction Database-TR version 2 Australia 8unstable0.77
miRdSNP - Database of Disease-associated SNPs and MicroRNA target Sites on 3'UTRs of Human Genes United States 59alive9.64
TiPs Italy 1alive0.20
CircuitsDB Italy 59unstable6.93
miRCancer - microRNA Cancer Association Database United States 80unstable12.48
UMD-CFTR - UMD-CFTR France 11alive1.35
GEPdb - Genotype-Expression-Phenotype Database Korea Rep. 1alive0.25
mitodyn - MITOchondrial DYNamics variation pages France 4alive1.33
LincSNP China 24alive5.76
MARMAL-AID - A Database for Infinium HumanMethylation450 United Kingdom 16alive3.17
MSigDB - Molecular Signatures Database United States 415unstable36.76
ExportAid - Database of RNA elements regulating nuclear RNA export in mammals Italy 1alive0.33
OncomiRDB(Tsinghua) - A Database for Oncogenic & Tumor-Suppressive MicroRNAs China 18unstable3.11
LOVD - Leiden Open Variation Database France 33dead0.00
SNP@lincTFBS - SNP in human lincRNA TFBS database China 3alive0.72
dbCerEx - database of Cervical Cancer Gene Expression China 0dead0.00
SurvExpress Mexico 37unstable5.40
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 3unstable0.26
hmChIP United States 28alive4.00
hPDI - Human Protein-DNA Interactome database United States 41alive5.02
HSC-explorer - hematopoietic stem cell explorer Germany 6unstable1.07
CLIPdb China 0alive0.00
INstruct United States 27alive5.35
dbCPCO - dbCPCO Canada 14alive1.73
FinDis - Finnish Disease Database Finland 7unstable1.25
IRView - Database and viewer of interacting regions (IRs) in protein sequences Japan 1alive0.17
IthaGenes - Interactive archive of all sequence variations affecting haemoglobin disorders Cyprus 5alive1.24
Liverome - A database of liver cancer-related gene lists Korea Rep. 19alive2.71
lnCeDB - lnCeDB India 15dead0.00
Hoppsigen - Homologous Processed Pseudogenes database France 44unstable0.34
NPRD - Nucleosome Positioning Region Database Russian Federation 20alive1.52
ECgene - ECgene Korea Rep. 167unstable6.29
SpliceInfo Taiwan 37alive2.73
DoOP - Database of Orthologous Promoters Hungary 37unstable1.76
TRED - Transcriptional Regulatory Element Database United States 155alive11.57
HuSiDa - human siRNA database Germany 43dead0.00
PolyA_DB United States 83alive6.38
RNAdb Australia 290unstable10.71
siRNAdb Sweden 55unstable3.26
SPD - Secreted Protein Database China 119unstable4.03
TPMD - Taiwan Polymorphic Marker Database Taiwan 6unstable0.30
GenDiS - Genomic Distribution of Protein Structural Domain Superfamilies India 16alive1.22
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
ChimerDB Korea Rep. 86unstable4.73
H-DBAS - Human-transcriptome Database for Alternative Splicing Japan 80alive7.27
deepBase - deepBase China 102unstable3.31
HHMD - Human Histone Modification Database China 42unstable4.72
L1Base Germany 78unstable5.04
DG-CST - Disease Gene Conserved Sequence Tags Database Italy 17alive1.29
HCAD - Human Chromosome Aberration Database Spain 10dead0.00
FESD - Functional Element SNPs Database Korea Rep. 35dead0.00
CGED - Cancer Gene Expression data Japan 46dead0.00
5'SAGE - 5'-end Serial Analysis of Gene Expression database Japan 17dead0.00
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
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive2.92
MITOMAP - A database for the human mitochondrial genome United States 325unstable20.25
DP - Dynamic Proteomics Israel 15dead0.00
HLungDB - Human Lung Cancer Database China 48dead0.12
HRTBLDb - Hormone Receptors Target Binding Loci Database United States 9dead0.00
SelTarbase Germany 42alive5.25
PLANdbAffy - probe-level annotation database for Affymetrix expression microarrays Russian Federation 28alive3.47
VBASE2 - VBASE2 Germany 104alive8.00
HUMHOT - Human Meiotic Recombination Hot Spots India 5dead0.00
The imprinted gene and parent-of-origin effect database New Zealand 551unstable19.01
ISfinder - Insertion Sequence finder France 455unstable7.20
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 112unstable7.19
TiProD China 27dead0.00
ARED Saudi Arabia 928unstable35.48
Argonaute Germany 88alive7.26
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
snoRNA-LBME-db France 297unstable4.70
LOCATE - subcellular localization database Australia 87alive7.25
NOPdb - Nucleolar Proteome Database United Kingdom 96dead0.00
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
LGICdb - Ligand-Gated Ion Channel database United Kingdom 18unstable1.30
OKCAM - Ontology for Cell Adhesion Molecules United States 10unstable1.04
SysZNF - the C2H2 zinc finger gene database Germany 31unstable0.59
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable124.58
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.64
ISED - Influenza Sequence and Epitope Database Korea Rep. 11alive1.22
PIG - Pathogen Interaction Gateway United States 55unstable1.16
PIPs - human protein–protein interaction prediction database United Kingdom 114alive12.67
VirusMINT - viral protein interaction database Italy 124unstable1.52
PID - Pathway Interaction Database United States 593unstable44.80
CleanEST Korea Rep. 14unstable1.42
EVOG - Evolution Visualizer for Overlapping Genes Korea Rep. 12alive1.33
ExDom - ExDom United States 10unstable0.23
HPRD - Human Protein Reference Database India 3067unstable192.20
Human Proteinpedia India 65unstable6.79
BodyParts3D Japan 30dead0.00
HGVbaseG2P - The Human Genome Variation database United Kingdom 63unstable5.32
SNPLogic United States 26unstable0.81
VarySysDB - VarySysDatabase Japan 16alive1.72
CTdatabase - Cancer-Testis Database Brazil 116unstable12.12
MoKCa - Mutations, Oncogenes, Knowledge & Cancer United Kingdom 34alive3.74
AutDB - Autism Spectrum Disorders database United States 121unstable11.97
ERGR - ethanol-related gene resource United States 32dead0.00
G2Cdb - Genes to Cognition database United Kingdom 41alive4.46
MDPD - Mutation Database for Parkinson's Disease Singapore 15unstable0.73
RAPID - Resource of Asian Primary Immunodeficiency Diseases India 33unstable3.45
Sys-BodyFluid China 57unstable1.08
SysPIMP China 16unstable0.11
CLDB - Cell Line Data Base Italy 61alive6.78
YH - YanHuang China 30unstable3.13
microTranspoGene - The influence of Transposed Elements (TEs) on the biogenesis of microRNAs Israel 56alive5.54
TranspoGene - TranspoGene Israel 56alive5.54 - and Expression United States 1199unstable94.72
PharmGKB - The Pharmacogenomics Knowledgebase United States 67unstable1.27
CEBS - Chemical Effects in Biological Systems United States 106unstable6.57
PubMeth Belgium 127alive12.57
MethyCancer - The Database of Human DNA Methylation and Cancer China 75alive7.43
CanGEM - Cancer GEnome Mine Finland 35unstable2.24
F-SNP - The Functional Single Nucleotide Polymorphism database Canada 242unstable18.63
MSY Breakpoint Mapper - A Database of Sequence-tagged Sites in Defining Naturally Occurring Deletions in the Human Y Chromosome United States 19alive1.88
Evola - Database of Evolutionary Features of Human Genes Japan 35alive3.50
IDBD - Infectious Disease Biomarker Database Korea Rep. 18unstable1.30
piRNABank - A web resource on classified and clustered Piwi-interacting RNAs India 111unstable10.43
Vir-Mir - The viral miRNA prediction database Taiwan 60alive5.88
ChromDB - The chromatin database United States 72unstable4.90
Greglist - Database of G-quadruplex Regulated Genes China 43unstable2.71
QuadBase - QuadBase India 71unstable6.46
PReMod - Predicted Regulatory Modules Canada 94alive8.37
Pseudogene United States 115unstable1.99
SNPSTR - microsatellite marker and tightly linked SNPs United Kingdom 31alive2.73
VEB - VISTA Enhancer Browser United States 340unstable10.20
GenomeTrafac - GenomeTrafac United States 25alive2.27
D-HaploDB - The Definitive Haplotype Database Japan 9unstable0.24
PolyDoms United States 58alive5.17
Snap - Single Nucleotide Polymorphism Annotation Platform Denmark 32alive2.79
CancerGenes - CancerGenes United States 151alive13.59
PharmGED - Pharmacogenetic Effect Database Singapore 8dead0.00
MAPU - Max-Planck Unified proteome database Germany 53unstable4.24
GAN - Gene Aging Nexus United States 38unstable1.04
EPConDB - EPConDB United States 15alive1.36
OncoDB.HCC - Oncogenomic Database of Hepatocellular Carcinoma Taiwan 61alive5.49
HSPD - Hedgehog Signaling Pathway Database United States 3dead0.00
GeneSpeed - GeneSpeed database United States 10dead0.00
eSLDB - eSLDB Italy 45alive4.09
GlycoMapsDB - GlycoMapsDB Germany 46alive4.18
TBestDB - Taxonomically Broad EST Database Canada 84alive7.56
QTL MatchMaker United States 5unstable0.34
CTGA - Catalogue of Transmission Genetics in Arabs United Arab Emirates 42alive3.50
HPtaa database China 18unstable0.50
ITTACA - Integrated Tumor Transcriptome Array and Clinical data Analysis France 43alive3.58
CAGE - Cap-analysis gene expression Japan 76alive6.33
PeptideAtlas United States 839alive69.22
MitoP2 - An integrative tool for the analysis of the mitochondrial proteome Germany 156dead0.00
OncomiRdbB - Oncogenic miRNA database India 1alive0.25
NetworKIN - A Resource for Exploring Cellular Phosphorylation Networks Canada 195alive19.50
DisProt - Database of Protein Disorder United States 838alive63.82
GenBank - GenBank United States 46415unstable492.28
HIV-1, human interaction database - Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database United States 386unstable13.51
RBP-Var China 0alive0.00
MERAV - Metabolic gEne RApid Visualizer United States 0alive0.00
TCGASpliceSeq - TCGASpliceSeq United States 0alive0.00
Aging Chart Russian Federation 0unstable0.00
CRN - Cancer RNA-Seq Nexus Taiwan 0alive0.00
UET - Universal Evolutionary Trace United States 1alive0.49
Lynx United States 0alive0.00
MutationAligner - A Resource of Recurrent Mutation Hotspots in Protein Domains in Cancer United States 0unstable0.00
DGIdb - Drug-Gene Interaction Database United States 78unstable9.52
DIANA-miRGen - DIANA-miRGen Greece 303unstable25.34
SORFS.ORG Belgium 2alive0.98
BreCAN-DB India 0alive0.00
piRNA cluster db - piRNA cluster database Germany 29unstable4.49
iGNM - Gaussian Network Model Database United States 116alive8.92
WeGET - Weighted Gene Expression Tool and database Netherlands 0unstable0.00
PCOSKB - KnowledgeBase on Polycystic Ovary Syndrome India 1alive0.49
SugarBindDB - SugarBind Database Switzerland 10alive1.98
SEA - Super-Enhancer Archive China 1alive0.50
Start2Fold Belgium 1alive0.50
hPSCreg - human pluripotent stem cell research community Germany 1alive0.50
DASHR - Database of small human noncoding RNAs United States 1alive0.48
WITHDRAWN - Database of withdrawn and discontinued drugs Germany 1alive0.50
miRNASNP - microRNA-related Single Nucleotide Polymorphisms China 145alive23.44
miRSponge - Experimentally validated miRNA Sponges database China 1unstable0.32
MGDB_2 - Melanoma Gene Database China 0unstable0.00
RegNetwork - Regulatory Network Repository United States 0alive0.00
DENdb - Dragon ENhancers database Saudi Arabia 1unstable0.27
MetazSecKB - Metazoa (Human/Animal) Secretome and Subcellular Proteome KnowledgeBase United States 0unstable0.00
NNTC - National NeuroAIDS Tissue Consortium United States 0unstable0.00
SHIELD - Shared Harvard Inner Ear Laboratory Database United States 0alive0.00
HMA - Human Metabolic Atlas Sweden 3alive0.99
EpiFactors - EpiFactors Russian Federation 3alive0.99
NeuroTransDB - Highly Curated and Structured Transcriptomic Metadata for Neurodegenerative Diseases Germany 1unstable0.06
FARE-CAFE - Database of Functional and Regulatory Elements of Cancer-Associated Fusion Events Taiwan 1unstable0.21
RBCC - Red Blood Cell Collection Hungary 1alive0.33
OCDB - Obsessive-Compulsive Disorder Database Italy 1unstable0.14
HCSD - Human Cancer Secretome Database Sweden 1alive0.32
dbSUPER - a database of super-enhancers in mouse and human genome China 2unstable0.93
ccmGDB - Cancer Cell Metabolism Gene DataBase United States 2unstable0.16
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
rVarBase China 28alive6.79
Colorectal Cancer Atlas Australia 1alive0.50
OpenTein - Open Teratoma Investigation Japan 0alive0.00
KLIFS Netherlands 2alive0.99
RMBase - RNA Modification Base China 2unstable0.59
Metabolomics Workbench United States 0alive0.00
SIGNOR - SIGnaling Network Open Resource Italy 2unstable0.75
DIDA - DIgenic diseases DAtabase Belgium 1alive0.50
Lnc2Cancer China 2alive0.96
GtoPdb - IUPHAR/BPS Guide to PHARMACOLOGY United Kingdom 2alive0.98
MitoCarta - An Inventory of Mammalian Mitochondrial Genes United States 2unstable0.50
DESSCD - Dragon Exploration System for Sickle Cell Disease Saudi Arabia 2unstable0.37
dPORE-miRNA - Dragon Database of Polymorphic Regulation of miRNA genes Saudi Arabia 25unstable3.29
DESMSCI - Marine sponge compounds interactions Saudi Arabia 5unstable0.92
DESTAF - Dragon Exploration System for Toxicants and Fertility Saudi Arabia 3unstable0.42
piRNAQuest - searching the piRNAome for silencers India 4alive0.99
WikiCell China 8unstable1.19
AlzBase - an integrative database for gene dys-regulation in Alzheimer’s disease China 5alive2.50
MTD - mammalian transcriptomic database China 0alive0.00
HGMD - The Human Gene Mutation Database United Kingdom 2655unstable98.61
BIG Data Center - BIG Data Center for Life & Health Sciences China 12alive12.00
GTRD - Gene Transcription Regulation Database Russian Federation 0alive0.00
LNCediting United States 0alive0.00
miRPathDB - miRNA Pathway Dictionary Database Germany 1dead0.00
POSTAR - POST-trAnscriptional Regulation China 1unstable0.95
R-loopDB Singapore 0alive0.00
SNP2TFBS Switzerland 0unstable0.00
TFBSbank United Kingdom 0unstable0.00
ADPriboDB - The Database of ADP-ribosylated proteins United States 0alive0.00
Membranome - Membrane Proteome United States 1unstable0.61
WERAM - Writers, Erasers and Readers of Acetylation & Methylation China 1alive1.00
COEXPEDIA Korea Rep. 0alive0.00
HIPPIE - Human Integrated Protein-Protein Interaction rEference Spain 49unstable5.00
3DSNP China 0unstable0.00
Cistrome DB - Cistrome Data Browser China 0alive0.00
GenomeCRISPR Germany 0alive0.00
HipSci - Human Induced Pluripotent Stem Cells Initiative United Kingdom 0alive0.00
REDIportal Italy 1alive1.00
AAgAtlas China 0alive0.00
mirDNMR China 1unstable0.87
denovo-db United States 0alive0.00
dbDEMC - database of Differentially Expressed MiRNAs in human Cancers China 54unstable4.72
dbSAP - Single Amino Acid Polymorphism Database China 0unstable0.00
IGSR - The International Genome Sample Resource United Kingdom 1alive1.00
HPO - Human Phenotype Ontology United States 975unstable72.15
NSDNA - The Nervous System Disease NcRNAome Atlas China 0unstable0.00
KERIS - The kaleidoscope of gene responses to inflammation among species United States 0alive0.00
SZGR - Schizophrenia Gene Resource United States 72dead0.00
Exposome-Explorer France 1alive0.99
dbWGFP China 1unstable0.44
CoReCG - Colon Rectal Cancer Gene Database India 0alive0.00
HLA-ADR - Human leukocyte antigens Adverse Drug Reaction Database United Kingdom 2alive1.00
GESDB - Genetic Epidemiology Simulation Database Taiwan 1unstable0.18
SinEx DB - SinEx DATABASE Chile 0alive0.00
SlideBase Denmark 0alive0.00
MDM-Portal - Medical Data Models Germany 7dead0.00
CCSI - Chromatin–Chromatin Spatial Interaction China 0unstable0.00
Wikidata United States 4dead0.00
CSCdb - Cancer stem cells database China 0unstable0.00
HNdb - Head and Deck Database Brazil 0alive0.00
BRONCO - Biomedical entity Relation ONcology COrpus Korea Rep. 7alive3.36
PepPSy France 0alive0.00
Tfcheckpoint - Transcription Factor Checkpoint Norway 8alive1.60
Harmonizome United States 5unstable2.28
TMC-SNPdb - Tata Memorial Centre-SNP data base India 1alive0.50
KDD - Kawasaki Disease Database Korea Rep. 0alive0.00
Onco-Regulon India 0alive0.00
peptiCKDdb Germany 0alive0.00
CaspNeuroD United States 0unstable0.00
KTCNlncDB Poland 0alive0.00
RAIN - RNA–protein Association and Interaction Networks Switzerland 3unstable0.99
PDID - Protein–Drug Interaction Database Canada 2unstable0.89
EpimiRBase Ireland 4unstable1.82
lnCaNet Australia 6alive3.00
BISQUE - Biological Sequence Exchange United States 1alive0.50
dbDSM - database of Deleterious Synonymous Mutation China 1unstable0.44
MINTbase United States 23dead0.00
PhenoScanner United Kingdom 6alive3.00
SSBD - Systems Science of Biological Dynamics database Japan 7alive2.33
LncVar - genetic variation associated with long non-coding genes China 2alive1.98
LD Hub United Kingdom 12alive11.88
NaviCom - Connects data to network maps France 12dead0.00
GVM - Genome Variation Map China 0alive0.00
VISTA Enhancer Browser - VISTA Enhancer Browser whole genome enhancer browser United States 0dead0.00
* Citations derived from Google Scholar.