Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
AnimalTFDB - Animal Transcription Factors Database China 82alive13.26
COXPRESdb - Coexpression Database Japan 230alive23.00
DIANA-TarBase - DIANA-TarBase Greece 1513alive126.08
DoRiNA - Database of RNA Interactions in Post-transcriptional Regulation Germany 115unstable15.72
TOPDB - Topology Database of Transmembrane Proteins
Hungary 57unstable3.42
MatrixDB - The extracellular matrix interaction database France 4alive1.32
BRENDA - The Comprehensive Enzyme Information System
Germany 706alive99.85
STRING - Known and Predicted Protein-Protein Interactions
Switzerland 9248alive513.78
Binding MOAD - Binding Mother of All Databases
United States 148alive11.27
BioGRID - Biological General Repository for Interaction Datasets
Canada 4359unstable261.54
Complex Portal
United Kingdom 0unstable0.00
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
DEPOD - Human DEPhOsphorylation Database Germany 0unstable0.00
HIV-1 Human Interaction Database United States 171unstable6.16
ViRBase - virus-host ncRna interaction database China 0alive0.00
VirHostNet - Virus-Host Network France 93unstable8.89
TrypanoCyc - Trypanosoma brucei Database France 0alive0.00
PHI-base - Pathogen-Host Interactions database United Kingdom 340alive28.05
RGD - Rat Genome Database United States 60unstable16.00
Xenbase - Xenopus model organism database Canada 214alive21.40
DAA - Digital Ageing Atlas United Kingdom 9alive3.00
T3DB - The Toxin and Toxin Target Database Canada 73alive9.13
EHFPI - Database of Essential Host Factors for Pathogenic Infection
China 1unstable0.21
CATdb - Complete Arabidopsis Transcriptome database France 0alive0.00
CODEX
United Kingdom 13alive4.29
GeneFriends - GeneFriends:RNAseq United Kingdom 31alive5.17
miRTarBase - miRNA Target Database Taiwan 899alive128.43
starBase - starBase China 491unstable55.41
NPInter - ncRNA Interaction Database China 119unstable8.13
YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking Portugal 793alive65.42
BloodChIP Australia 11unstable0.85
Network portal - A Database for Storage, Analysis and Visualization of Biological Networks
United States 14alive3.47
iPfam - Catalog of Protein Family Interactions
United States 38unstable4.84
3did - 3-Dimensional Interacting Domains
Spain 399unstable20.56
FunCoup - Database of Genome-wide Functional Coupling Networks.
Sweden 73alive11.92
STITCH - Search Tool for Interacting Chemicals
Germany 624alive62.40
UniHI - Unified Human Interactome Portugal 194alive17.64
SMPDB - The Small Molecule Pathway Database Canada 110alive13.48
EKPD - Database of Eukaryotic Protein Kinases China 12alive3.00
ASD - Allosteric Database
China 94alive13.43
SubtiWiki - A community resource for the model organism Bacillus subtilis Germany 159alive17.49
SGD - Saccharomyces Genome Database United States 772alive128.67
YeastNet - Probabilistic Functional Gene Network of Saccharomyces cerevisiae Korea Rep. 17unstable3.53
VEGA - Vertebrate Genome Annotation United Kingdom 368unstable25.19
WormBase - WormBase Canada 2150alive126.47
Manteia France 18alive4.50
canSAR United Kingdom 70unstable10.85
VIOLIN - Vaccine investigation and online information network United States 20alive5.00
Gramene - A comparative resource for plants United States 79alive19.75
P3DB - Plant Protein Phosphorylation DataBase United States 129alive14.05
Factorbook - Factorbook United States 61unstable2.44
ChIPBase China 199unstable25.87
CTCFBSDB - CTCF Binding Sites and Genome Organization Database United States 118alive11.68
BSRD - Bacteria Small Regulatory RNA Database Hong Kong SAR China 27alive5.29
DIANA-LncBase - Database on miRNA-lncRNA interactions Greece 98unstable17.25
dbPTM - Database of Protein Post-Translational Modifications
Taiwan 205alive16.91
ValidNESs - Validated NES-containing proteins, functional NES sites and NES predictions Taiwan 21unstable3.91
The Genome Properties database - The Genome Properties database United States 65unstable12.09
ChemProt - Chemical-protein Interaction Database
Denmark 97alive13.44
SIFTS - Structure Integration with Function, Taxonomy and Sequence
United Kingdom 50alive10.00
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.14
DGA - Database of Disease and Gene Annotations China 23unstable3.82
ViralZone - ViralZone Switzerland 76unstable8.69
dictyBase - Database for Dictyostelium Discoideum United States 128alive14.08
NetwoRx - Connecting Drugs to Networks and Phenotypes in Saccharomyces Cerevisiae Canada 6alive1.19
enzyme portal - enzyme portal
United Kingdom 13unstable1.85
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161unstable17.98
WholeCellKB - WholeCellKB United States 16alive3.20
CPDB - Consensus Pathway Database Germany 368unstable28.21
2P2IDB - Protein-Protein Interaction Inhibition Database
France 321alive39.72
PrePPI - A structure-informed database of protein-protein interactions United States 301unstable13.55
SynSysNet - Synaptic Proteins Database Germany 18alive3.60
TissueNet - The Database of Human Tissue Protein-Protein Interactions Israel 53alive10.39
GTR - National Institutes of Health Genetic Testing Registry United States 33unstable2.44
TSGene - tumor suppressor gene database United States 89unstable3.38
SomamiR United States 27alive5.35
METscout - METscout
Germany 2alive0.40
BioLiP
United States 63alive12.60
G4LDB - G-quadruplex ligands database China 24unstable2.93
RiceFREND - Rice Functionally Related Gene Expression Network Database Japan 29unstable5.16
InnateDB Canada 339unstable29.49
DOR - DDBJ Omics Archive
Japan 35unstable4.72
MAPPER2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation United States 116unstable5.89
SitEx Russian Federation 5alive0.82
DD - Database of Death Domain Korea Rep. 14alive2.33
DOMMINO - Database of MacroMolecular Interactions
United States 14unstable1.17
ProtChemSI - protein-chemical structural interactions Germany 9alive1.49
ViPR - virus pathogene resourse United States 57alive9.50
CoryneRegNet - Corynebacterial Transcription Factors and Gene Regulatory Networks Germany 202unstable7.91
VFDB - Virulence Factor Database China 448alive34.46
FungiDB - FungiDB United States 47alive7.68
Nematode - Nematode.net United States 163alive11.64
MMMDB - Mouse Multiple tissue Metabolome DataBase Japan 17alive2.83
IBIS - Inferred Biomolecular Interactions Server
United States 33alive5.45
IntAct United Kingdom 499unstable56.55
PINA - Protein Interaction Network Analysis Australia 281unstable24.04
Predictive networks United States 24unstable3.52
NCG - Network of Cancer Genes Italy 51alive8.50
GeneWeaver - GeneWeaver United States 54alive8.73
SuperTarget
Germany 273unstable6.55
MetaCrop - Metabolic pathways in crop plants Germany 73alive7.23
DIGIT - Database of ImmunoGlobulins with Integrated Tools Italy 19alive3.10
AREsite - AU-rich Elements Site Austria 110alive15.56
TcoF-DB - Dragon database of transcription co-factors and transcription factor interacting proteins Saudi Arabia 36alive4.94
CLIPZ - Cross-linking and Immunoprecipitation
Switzerland 72unstable8.95
PRIDB - Protein-RNA Interface Database United States 49unstable6.44
ThYme - Thioester-active Enzymes
United States 30alive4.29
VKCDB - voltage-gated potassium channels databse Canada 34alive2.43
TADB - Toxin-antitoxin Data Base China 94unstable12.49
Pathway Commons - Search and visualize public biological pathway information United States 395alive56.43
BISC - BInary SubComplex Database
United Kingdom 3unstable0.12
DIMA - Domain Interaction MAp
Germany 69unstable4.54
DOMINE - Database of Protein Domain Interaction
United States 205unstable12.09
DroID - Drosophila Interactions Database United States 183alive18.12
KUPS - University of Kansas Proteomics Service United States 21unstable0.36
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.43
RegPhos - Regulatory Network in Protein Phosphorylation Taiwan 49alive6.93
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
CancerResource Germany 59alive8.34
The Autophagy Database Japan 25dead0.00
FragmentStore - FragmentStore
Germany 11alive1.57
PROMISCUOUS Germany 109alive15.57
AGRIS - Arabidopsis Gene Regulatory Information Server United States 701unstable44.40
AtPID - Arabidopsis thaliana Protein Interactome Database China 136unstable12.10
PAIR - Predicted Arabidopsis Interactome Resource China 32unstable1.23
human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactions Germany 14alive1.73
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.63
AthaMap - Arabidopsis thaliana Map Germany 275alive19.45
NetSlim - High-confidence Curated Signaling Maps
United States 18unstable2.31
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
India 14alive2.00
CTD - Comparative Toxicogenomics Database United States 1016alive67.73
eFIP - eFIPonline
United States 13unstable1.75
Aptamer base - Aptamer database
Canada 21unstable1.54
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.16
CoIN - Co-occurrence Interaction Nexus
Taiwan 2dead0.00
yApoptosis - yeast apoptosis database Sweden 1alive0.20
CARLSBAD United States 5alive0.98
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable0.94
PPInterFinder - Protein-Protein Interactions Finder India 17unstable0.20
CREDO
United Kingdom 11unstable1.78
T2D@ZJU - Type 2 Diabetes Database at Zhejiang University China 6unstable0.35
CHD@ZJU - Coronary Heart Disease Research Platform China 7unstable0.64
AIM - Arabidopsis Interactome Modules Database United States 0unstable0.00
DEOP - Database on Osmoprotectants and Associated Pathways Saudi Arabia 4unstable0.93
MetaProx - The Database of Metagenomic Proximons Canada 2alive0.50
Mouse IDGenes - Gene interactions in the developing mouse brain Germany 1alive0.25
YTRP - Yeast Transcriptional Regulatory Pathway Taiwan 5alive1.23
BambooGDB - Bamboo Genome Database China 12unstable1.47
TSLP signaling pathway map - Thymic stromal lymphopoietin signaling pathway map United States 10unstable2.28
RegaDB - Rega database South Africa 2unstable0.38
ANIA - ANnotation and Integrated Analysis of the 14-3-3 interactome United Kingdom 6unstable0.31
PLIC - Protein-Ligand Interaction Clusters India 3alive0.74
SoyFN - A Knowledge Database of Soybean Functional Networks China 3unstable0.52
EcoliNet - Database of Cofunctional Gene Network for Escherichia coli Korea Rep. 0unstable0.00
CBN - Causal biological network database Switzerland 7alive2.24
novPTMenzy - A Database for Enzymes Involved in Novel Post-translational Modifications.
India 1unstable0.31
MIsoMine - A data portal of expression,function and network of splice isoforms in the mouse United States 3alive0.99
AtmiRNET Taiwan 3alive0.99
GraP - Platform of Functional Genomics Analysis in Gossypium raimondii China 1unstable0.30
3DGD - 3D Genome Database China 6unstable0.72
ConsensusPathDB Germany 368unstable27.80
3D-interologs - 3D-domain interactions based on homologous proteins
Taiwan 18alive2.25
SKEMPI - Structual database of Kinetics and Energetics of Mutant Protein Interactions
Spain 53alive8.74
VTCdb - ViTis Co-expression DataBase Australia 10unstable1.74
IIIDB - database for isoform-isoform interactions and isoform network modules
United States 0alive0.00
MPID-T2 - MHC-Peptide Interaction Database-TR version 2 Australia 8unstable0.74
CircuitsDB Italy 59unstable6.93
CAP - Citrus sinensis Annotation Project China 8alive1.98
TRIP - TRansient receptor potential channel-Interacting Protein
Korea Rep. 34alive4.76
CMRegNet Brazil 0alive0.00
CLIPdb China 0alive0.00
INstruct United States 27alive5.35
DBBP - DataBase of Binding Pairs in protein-nucleic acid interactions Skip Navigation Links
Korea Rep. -unstable-
footprintDB - footprintDB
Spain 9alive2.25
PDBSITE Russian Federation 92alive7.01
CYGD - Comprehensive Yeast Genome Database Germany 327unstable21.38
GeneNet - The GeneNet system Russian Federation 68alive5.18
3D-footprint
Spain 34alive4.25
RegPrecise - Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes United States 141unstable14.28
TransmiR - TF–miRNA Regulatory Database
China 184alive22.77
SuperCYP
Germany 102alive12.75
UM-BBD - University of Minnesota Biocatalysis/Biodegradation Database United States 94dead0.00
DRYGIN - Data Repository of Yeast Genetic Interactions Canada 71alive8.70
GWIDD - Genome-wide Protein Docking Database
United States 30alive3.71
PepX - A structural database of non-redundant protein-peptide complexes Belgium 60unstable6.22
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable224.25
PINT - Protein–protein Interactions Thermodynamic Database Japan 57unstable3.37
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable11.49
BIOZON
United States 53unstable4.02
miRecords - An Integrated Resource for MicroRNA-target Interactions United States 745dead0.00
siRecords United States 20unstable0.33
PiSite - Database of Protein Interaction Sites Japan 28alive3.11
RsiteDB - RNA binding site database
Israel 19alive2.09
PMAP - The Proteolysis MAP United States 31unstable1.93
EcID - Escherichia coli Interaction Database Spain 26alive2.89
KDBI - Kinetic Data of Biomolecular Interactions
Singapore 13alive1.42
MiMI - Michigan Molecular Interactions
United States 85unstable3.31
PIG - Pathogen Interaction Gateway United States 55unstable1.28
PIPs - human protein–protein interaction prediction database United Kingdom 114alive12.67
VirusMINT - viral protein interaction database Italy 124unstable1.65
AutDB - Autism Spectrum Disorders database United States 121unstable12.10
DBTBS - Database of Transcriptional Regulation in Bacillus subtilis Japan 495alive29.12
TransfactomeDB - Yeast Transfactome Database United States 22alive2.18
TAIR - The Arabidopsis Information Resource United States 768unstable43.01
GLIDA - GPCR-Ligand Database
Japan 95alive9.50
EndoNet - EndoNet
Germany 24alive1.98
Bacteriome.org - Bacteriome.org Canada 46unstable2.07
BioHealthBase United States 70unstable5.11
DB-PABP - DB-PABP
United States 4dead0.00
SNAPPI-DB - SNAPPI-DB
United Kingdom 60alive5.45
WormBook - the online review of Caenorhabditis elegans biology United States 51alive4.64
DOMINO - DOMINO
Italy 72unstable1.05
LMSD - LIPID MAPS Structure Database
United States 279alive25.36
CYCLONET - CYCLONET
Russian Federation 15alive1.36
CellCircuits
United States 35unstable2.16
BindingDB - BindingDB
United States 706alive61.61
MPact - MIPS Protein Interaction Resource on Yeast Germany 357unstable9.82
pSTIING United Kingdom 47alive3.92
TRANSPATH - a database of mammalian signal transduction and metabolic pathways Germany 849unstable4.02
MfunGD - MIPS Mouse Functional Genome Database Germany 14unstable0.41
Epitome - Epitome
United States 58unstable3.82
RegTransBase - a database of regulatory sequences and interactions United States 104unstable1.99
NetworKIN - A Resource for Exploring Cellular Phosphorylation Networks Canada 195alive19.50
HIV-1, human interaction database - Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database United States 386unstable14.28
RBP-Var China 0alive0.00
CRN - Cancer RNA-Seq Nexus Taiwan 0alive0.00
Lynx United States 0alive0.00
IC4R - Information Commons for Rice China 1alive0.50
DGIdb - Drug-Gene Interaction Database United States 78unstable10.14
DIANA-miRGen - DIANA-miRGen Greece 303unstable25.34
EBI - The European Bioinformatics Institute United Kingdom 610unstable17.28
SugarBindDB - SugarBind Database Switzerland 10alive1.98
GEneSTATION United States 1alive0.48
InterRNA - INTERactions in RNA structures database
Malaysia 0alive0.00
MtiBase - MiRNA-target interactions database
China 0unstable0.00
RegNetwork - Regulatory Network Repository United States 0alive0.00
LncReg - database for LncRNA regulating
China 2unstable0.59
SInCRe - Structural Interactome Computational Resource United Kingdom 0alive0.00
FARE-CAFE - Database of Functional and Regulatory Elements of Cancer-Associated Fusion Events Taiwan 1unstable0.22
KIR - Kiwifruit Information Resource China 0unstable0.00
MouseNet - Probabilistic Functional Gene Network for Laboratory Mouse,Mus Musculus Korea Rep. 0unstable0.00
READDB - RNA Binding Protein Expression and Disease Dynamics database
United States 0alive0.00
ccmGDB - Cancer Cell Metabolism Gene DataBase United States 2unstable0.17
SynLethDB Singapore 1unstable0.47
NBDB - Nucleotide binding database
Singapore 1alive0.48
sRNATarBase - sRNATarBase China 32unstable2.44
rVarBase China 28alive6.79
KLIFS Netherlands 2alive0.99
CircNet
Taiwan 0unstable0.00
SIGNOR - SIGnaling Network Open Resource Italy 2unstable0.80
SIDER - Side Effect Resource
Germany 2alive1.00
Lnc2Cancer China 2unstable0.95
FLOR-ID - Flowering Interactive Database Belgium 4alive2.00
PlantPAN - Plant Promoter Analysis Navigator Taiwan 188alive18.80
GtoPdb - IUPHAR/BPS Guide to PHARMACOLOGY United Kingdom 2alive0.98
HCVpro - Hepatitis C Virus Protein Interaction Database South Africa -unstable-
AlzBase - an integrative database for gene dys-regulation in Alzheimer’s disease China 5alive2.50
GTRD - Gene Transcription Regulation Database Russian Federation 0alive0.00
LNCediting United States 0alive0.00
POSTAR - POST-trAnscriptional Regulation China 1unstable0.95
RAID - RNA Association Interaction Database China 34alive8.50
SNP2TFBS Switzerland 0unstable0.00
mutLBSgeneDB - mutated Ligand Binding Site gene DataBase
United States 1alive1.00
HIPPIE - Human Integrated Protein-Protein Interaction rEference Spain 49unstable5.59
pathDIP - Pathway Data Integration Portal
Canada 1unstable0.94
XTalkDB
United States 0alive0.00
3DSNP China 0unstable0.00
SoyNet Korea Rep. 0unstable0.00
ccNET China 0unstable0.00
DrumPID - drug-minded protein interaction database
Germany 3alive1.50
HPIDB - Host - Pathogen Interaction Database United States 79alive9.78
CCSI - Chromatin–Chromatin Spatial Interaction China 0unstable0.00
ATtRACT
Spain 2unstable0.87
UbiNet - Ubiquitylation Networks Taiwan 1alive0.49
Abasy Atlas - Across-bacteria systems Atlas Mexico 1unstable0.47
DDRprot Spain 2unstable0.38
BELIEF - Biological Expression Language Information Extraction WorkFlow
Germany 0unstable0.00
PCPPI - Penicillium-Crop Protein-Protein Interactions database China 0unstable0.00
RAIN - RNA–protein Association and Interaction Networks Switzerland 3unstable1.11
PathwaysWeb
United States 0alive0.00
PDID - Protein–Drug Interaction Database Canada 2unstable0.88
lnCaNet Australia 6alive3.00
cMapper Korea Rep. 0alive0.00
NaviCom - Connects data to network maps France 12dead0.00
* Citations derived from Google Scholar.
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