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 82alive15.91
COXPRESdb - Coexpression Database Japan 230alive25.56
DIANA-TarBase - DIANA-TarBase Greece 1513alive137.55
DoRiNA - Database of RNA Interactions in Post-transcriptional Regulation Germany 115alive22.77
TOPDB - Topology Database of Transmembrane Proteins
Hungary 57unstable5.45
MatrixDB - The extracellular matrix interaction database France 4alive1.98
BRENDA - The Comprehensive Enzyme Information System
Germany 706alive116.49
STRING - Known and Predicted Protein-Protein Interactions
Switzerland 9248alive544.00
Binding MOAD - Binding Mother of All Databases
United States 148alive12.21
BioGRID - Biological General Repository for Interaction Datasets
Canada 4359alive396.27
Complex Portal
United Kingdom 0alive0.00
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
DEPOD - Human DEPhOsphorylation Database Germany 0unstable0.00
HIV-1 Human Interaction Database United States 171unstable9.88
ViRBase - virus-host ncRna interaction database China 0alive0.00
VirHostNet - Virus-Host Network France 93unstable9.88
TrypanoCyc - Trypanosoma brucei Database France 0alive0.00
PHI-base - Pathogen-Host Interactions database United Kingdom 340alive30.60
RGD - Rat Genome Database United States 60alive29.70
Xenbase - Xenopus model organism database Canada 214alive23.78
DAA - Digital Ageing Atlas United Kingdom 9alive4.50
T3DB - The Toxin and Toxin Target Database Canada 73alive10.43
EHFPI - Database of Essential Host Factors for Pathogenic Infection
China 1unstable0.44
CATdb - Complete Arabidopsis Transcriptome database France 0alive0.00
CODEX
United Kingdom 13alive6.43
GeneFriends - GeneFriends:RNAseq United Kingdom 31alive6.20
miRTarBase - miRNA Target Database Taiwan 899alive149.83
starBase - starBase China 491unstable68.74
NPInter - ncRNA Interaction Database China 119alive10.60
YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking Portugal 793alive71.37
BloodChIP Australia 11unstable1.65
Network portal - A Database for Storage, Analysis and Visualization of Biological Networks
United States 14alive4.67
iPfam - Catalog of Protein Family Interactions
United States 38unstable9.25
3did - 3-Dimensional Interacting Domains
Spain 399alive31.92
FunCoup - Database of Genome-wide Functional Coupling Networks.
Sweden 73alive14.31
STITCH - Search Tool for Interacting Chemicals
Germany 624alive69.33
UniHI - Unified Human Interactome Portugal 194alive19.40
SMPDB - The Small Molecule Pathway Database Canada 110alive15.40
EKPD - Database of Eukaryotic Protein Kinases China 12alive4.00
ASD - Allosteric Database
China 94alive15.67
SubtiWiki - A community resource for the model organism Bacillus subtilis Germany 159alive19.68
SGD - Saccharomyces Genome Database United States 772alive154.40
YeastNet - Probabilistic Functional Gene Network of Saccharomyces cerevisiae Korea Rep. 17alive5.67
VEGA - Vertebrate Genome Annotation United Kingdom 368alive30.36
WormBase - WormBase Canada 2150alive134.38
Manteia France 18alive6.00
canSAR United Kingdom 70unstable13.30
VIOLIN - Vaccine investigation and online information network United States 20alive6.67
Gramene - A comparative resource for plants United States 79alive26.33
P3DB - Plant Protein Phosphorylation DataBase United States 129alive16.13
Factorbook - Factorbook United States 61unstable4.27
ChIPBase China 199unstable30.35
CTCFBSDB - CTCF Binding Sites and Genome Organization Database United States 118alive12.98
BSRD - Bacteria Small Regulatory RNA Database Hong Kong SAR China 27alive6.62
DIANA-LncBase - Database on miRNA-lncRNA interactions Greece 98unstable20.58
dbPTM - Database of Protein Post-Translational Modifications
Taiwan 205alive18.64
ValidNESs - Validated NES-containing proteins, functional NES sites and NES predictions Taiwan 21unstable4.83
The Genome Properties database - The Genome Properties database United States 65unstable14.79
ChemProt - Chemical-protein Interaction Database
Denmark 97alive15.84
SIFTS - Structure Integration with Function, Taxonomy and Sequence
United Kingdom 50alive12.50
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.55
DGA - Database of Disease and Gene Annotations China 23alive5.75
ViralZone - ViralZone Switzerland 76alive12.67
dictyBase - Database for Dictyostelium Discoideum United States 128alive16.00
NetwoRx - Connecting Drugs to Networks and Phenotypes in Saccharomyces Cerevisiae Canada 6alive1.49
enzyme portal - enzyme portal
United Kingdom 13alive3.25
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161alive30.91
WholeCellKB - WholeCellKB United States 16alive4.00
CPDB - Consensus Pathway Database Germany 368unstable25.30
2P2IDB - Protein-Protein Interaction Inhibition Database
France 321alive45.40
PrePPI - A structure-informed database of protein-protein interactions United States 301unstable23.48
SynSysNet - Synaptic Proteins Database Germany 18alive4.50
TissueNet - The Database of Human Tissue Protein-Protein Interactions Israel 53alive12.99
GTR - National Institutes of Health Genetic Testing Registry United States 33unstable4.29
TSGene - tumor suppressor gene database United States 89unstable5.78
SomamiR United States 27alive6.68
METscout - METscout
Germany 2alive0.50
BioLiP
United States 63alive15.75
G4LDB - G-quadruplex ligands database China 24unstable2.94
RiceFREND - Rice Functionally Related Gene Expression Network Database Japan 29alive7.03
InnateDB Canada 339unstable30.89
DOR - DDBJ Omics Archive
Japan 35alive6.93
MAPPER2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation United States 116unstable9.18
SitEx Russian Federation 5alive0.99
DD - Database of Death Domain Korea Rep. 14alive2.80
DOMMINO - Database of MacroMolecular Interactions
United States 14unstable0.81
ProtChemSI - protein-chemical structural interactions Germany 9alive1.78
ViPR - virus pathogene resourse United States 57alive11.40
CoryneRegNet - Corynebacterial Transcription Factors and Gene Regulatory Networks Germany 202unstable12.30
VFDB - Virulence Factor Database China 448alive37.33
FungiDB - FungiDB United States 47alive9.40
Nematode - Nematode.net United States 163alive12.54
MMMDB - Mouse Multiple tissue Metabolome DataBase Japan 17alive3.40
IBIS - Inferred Biomolecular Interactions Server
United States 33alive6.60
IntAct United Kingdom 499alive97.80
PINA - Protein Interaction Network Analysis Australia 281unstable23.53
Predictive networks United States 24unstable4.18
NCG - Network of Cancer Genes Italy 51alive10.20
GeneWeaver - GeneWeaver United States 54alive10.80
SuperTarget
Germany 273unstable10.31
MetaCrop - Metabolic pathways in crop plants Germany 73alive8.03
DIGIT - Database of ImmunoGlobulins with Integrated Tools Italy 19alive3.69
AREsite - AU-rich Elements Site Austria 110alive18.15
TcoF-DB - Dragon database of transcription co-factors and transcription factor interacting proteins Saudi Arabia 36unstable5.70
CLIPZ - Cross-linking and Immunoprecipitation
Switzerland 72unstable9.72
PRIDB - Protein-RNA Interface Database United States 49unstable7.27
ThYme - Thioester-active Enzymes
United States 30alive5.00
VKCDB - voltage-gated potassium channels databse Canada 34alive2.62
TADB - Toxin-antitoxin Data Base China 94unstable14.41
Pathway Commons - Search and visualize public biological pathway information United States 395alive65.83
BISC - BInary SubComplex Database
United Kingdom 3unstable0.20
DIMA - Domain Interaction MAp
Germany 69unstable4.52
DOMINE - Database of Protein Domain Interaction
United States 205unstable19.13
DroID - Drosophila Interactions Database United States 183alive20.33
KUPS - University of Kansas Proteomics Service United States 21unstable0.59
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.67
RegPhos - Regulatory Network in Protein Phosphorylation Taiwan 49alive8.09
REPAIRtoire - A Database of DNA Repair Pathways Poland 24alive3.96
SPIKE - Signaling Pathways Integrated Knowledge Engine Israel 38alive6.33
FANTOM - Functional and taxonomic analysis of metagenomes Japan 144alive9.50
CancerResource Germany 59alive9.73
The Autophagy Database Japan 25dead0.00
FragmentStore - FragmentStore
Germany 11alive1.83
PROMISCUOUS Germany 109alive18.17
AGRIS - Arabidopsis Gene Regulatory Information Server United States 701alive50.07
AtPID - Arabidopsis thaliana Protein Interactome Database China 136alive14.51
PAIR - Predicted Arabidopsis Interactome Resource China 32unstable1.17
human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactions Germany 14alive1.98
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.86
AthaMap - Arabidopsis thaliana Map Germany 275alive20.94
NetSlim - High-confidence Curated Signaling Maps
United States 18unstable2.73
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
India 14alive2.33
CTD - Comparative Toxicogenomics Database United States 1016alive72.57
eFIP - eFIPonline
United States 13alive2.55
Aptamer base - Aptamer database
Canada 21unstable1.22
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.31
CoIN - Co-occurrence Interaction Nexus
Taiwan 2dead0.00
yApoptosis - yeast apoptosis database Sweden 1alive0.25
CARLSBAD United States 5alive1.23
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable1.58
PPInterFinder - Protein-Protein Interactions Finder India 17unstable0.38
CREDO
United Kingdom 11alive2.64
T2D@ZJU - Type 2 Diabetes Database at Zhejiang University China 6unstable0.62
CHD@ZJU - Coronary Heart Disease Research Platform China 7unstable0.72
AIM - Arabidopsis Interactome Modules Database United States 0unstable0.00
DEOP - Database on Osmoprotectants and Associated Pathways Saudi Arabia 4unstable1.24
MetaProx - The Database of Metagenomic Proximons Canada 2alive0.67
Mouse IDGenes - Gene interactions in the developing mouse brain Germany 1alive0.33
YTRP - Yeast Transcriptional Regulatory Pathway Taiwan 5alive1.63
BambooGDB - Bamboo Genome Database China 12unstable2.84
TSLP signaling pathway map - Thymic stromal lymphopoietin signaling pathway map United States 10unstable3.10
RegaDB - Rega database South Africa 2unstable0.44
ANIA - ANnotation and Integrated Analysis of the 14-3-3 interactome United Kingdom 6unstable0.58
PLIC - Protein-Ligand Interaction Clusters India 3alive0.99
SoyFN - A Knowledge Database of Soybean Functional Networks China 3unstable0.89
EcoliNet - Database of Cofunctional Gene Network for Escherichia coli Korea Rep. 0unstable0.00
CBN - Causal biological network database Switzerland 7unstable3.29
novPTMenzy - A Database for Enzymes Involved in Novel Post-translational Modifications.
India 1unstable0.45
MIsoMine - A data portal of expression,function and network of splice isoforms in the mouse United States 3alive1.49
AtmiRNET Taiwan 3alive1.49
GraP - Platform of Functional Genomics Analysis in Gossypium raimondii China 1unstable0.47
3DGD - 3D Genome Database China 6unstable1.00
ConsensusPathDB Germany 368unstable25.30
3D-interologs - 3D-domain interactions based on homologous proteins
Taiwan 18alive2.57
SKEMPI - Structual database of Kinetics and Energetics of Mutant Protein Interactions
Spain 53alive10.60
VTCdb - ViTis Co-expression DataBase Australia 10alive2.50
IIIDB - database for isoform-isoform interactions and isoform network modules
United States 0alive0.00
MPID-T2 - MHC-Peptide Interaction Database-TR version 2 Australia 8unstable0.67
CircuitsDB Italy 59alive8.34
CAP - Citrus sinensis Annotation Project China 8alive2.64
TRIP - TRansient receptor potential channel-Interacting Protein
Korea Rep. 34alive5.55
CMRegNet Brazil 0alive0.00
CLIPdb China 0alive0.00
INstruct United States 27alive6.68
DBBP - DataBase of Binding Pairs in protein-nucleic acid interactions Skip Navigation Links
Korea Rep. -unstable-
footprintDB - footprintDB
Spain 9alive3.00
PDBSITE Russian Federation 92alive7.59
CYGD - Comprehensive Yeast Genome Database Germany 327unstable21.53
GeneNet - The GeneNet system Russian Federation 68alive5.61
3D-footprint
Spain 34alive4.86
RegPrecise - Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes United States 141unstable18.73
TransmiR - TF–miRNA Regulatory Database
China 184alive26.29
SuperCYP
Germany 102alive14.57
UM-BBD - University of Minnesota Biocatalysis/Biodegradation Database United States 94dead0.00
DRYGIN - Data Repository of Yeast Genetic Interactions Canada 71alive9.84
GWIDD - Genome-wide Protein Docking Database
United States 30alive4.20
PepX - A structural database of non-redundant protein-peptide complexes Belgium 60alive8.57
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable180.71
PINT - Protein–protein Interactions Thermodynamic Database Japan 57unstable3.99
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable10.26
BIOZON
United States 53unstable4.24
miRecords - An Integrated Resource for MicroRNA-target Interactions United States 745dead0.00
siRecords United States 20unstable0.23
PiSite - Database of Protein Interaction Sites Japan 28alive3.50
RsiteDB - RNA binding site database
Israel 19alive2.38
PMAP - The Proteolysis MAP United States 31unstable3.02
EcID - Escherichia coli Interaction Database Spain 26alive3.25
KDBI - Kinetic Data of Biomolecular Interactions
Singapore 13alive1.58
MiMI - Michigan Molecular Interactions
United States 85unstable5.31
PIG - Pathogen Interaction Gateway United States 55unstable1.99
PIPs - human protein–protein interaction prediction database United Kingdom 114alive14.25
VirusMINT - viral protein interaction database Italy 124unstable2.63
AutDB - Autism Spectrum Disorders database United States 121unstable13.76
DBTBS - Database of Transcriptional Regulation in Bacillus subtilis Japan 495alive30.94
TransfactomeDB - Yeast Transfactome Database United States 22alive2.44
TAIR - The Arabidopsis Information Resource United States 768unstable67.41
GLIDA - GPCR-Ligand Database
Japan 95alive10.56
EndoNet - EndoNet
Germany 24alive2.16
Bacteriome.org - Bacteriome.org Canada 46unstable3.27
BioHealthBase United States 70unstable7.31
DB-PABP - DB-PABP
United States 4dead0.00
SNAPPI-DB - SNAPPI-DB
United Kingdom 60alive6.00
WormBook - the online review of Caenorhabditis elegans biology United States 51alive5.10
DOMINO - DOMINO
Italy 72unstable1.66
LMSD - LIPID MAPS Structure Database
United States 279alive27.90
CYCLONET - CYCLONET
Russian Federation 15alive1.50
CellCircuits
United States 35unstable2.03
BindingDB - BindingDB
United States 706alive69.19
MPact - MIPS Protein Interaction Resource on Yeast Germany 357unstable15.58
pSTIING United Kingdom 47alive4.27
TRANSPATH - a database of mammalian signal transduction and metabolic pathways Germany 849unstable6.13
MfunGD - MIPS Mouse Functional Genome Database Germany 14unstable0.64
Epitome - Epitome
United States 58unstable3.69
RegTransBase - a database of regulatory sequences and interactions United States 104unstable3.12
NetworKIN - A Resource for Exploring Cellular Phosphorylation Networks Canada 195alive21.67
HIV-1, human interaction database - Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database United States 386unstable22.30
RBP-Var China 0alive0.00
CRN - Cancer RNA-Seq Nexus Taiwan 0alive0.00
Lynx United States 0alive0.00
IC4R - Information Commons for Rice China 1alive1.00
DGIdb - Drug-Gene Interaction Database United States 78unstable18.14
DIANA-miRGen - DIANA-miRGen Greece 303unstable27.27
EBI - The European Bioinformatics Institute United Kingdom 610alive25.99
SugarBindDB - SugarBind Database Switzerland 10alive2.50
GEneSTATION United States 1alive0.98
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 2unstable0.91
SInCRe - Structural Interactome Computational Resource United Kingdom 0alive0.00
FARE-CAFE - Database of Functional and Regulatory Elements of Cancer-Associated Fusion Events Taiwan 1unstable0.38
KIR - Kiwifruit Information Resource China 0alive0.00
MouseNet - Probabilistic Functional Gene Network for Laboratory Mouse,Mus Musculus Korea Rep. 0alive0.00
READDB - RNA Binding Protein Expression and Disease Dynamics database
United States 0alive0.00
ccmGDB - Cancer Cell Metabolism Gene DataBase United States 2unstable0.48
SynLethDB Singapore 1unstable0.92
NBDB - Nucleotide binding database
Singapore 1alive0.99
sRNATarBase - sRNATarBase China 32unstable4.02
rVarBase China 28alive9.24
KLIFS Netherlands 2alive1.96
CircNet
Taiwan 0alive0.00
SIGNOR - SIGnaling Network Open Resource Italy 2alive1.94
SIDER - Side Effect Resource
Germany 2alive2.00
Lnc2Cancer China 2unstable1.86
FLOR-ID - Flowering Interactive Database Belgium 4alive4.00
PlantPAN - Plant Promoter Analysis Navigator Taiwan 188alive20.89
GtoPdb - IUPHAR/BPS Guide to PHARMACOLOGY United Kingdom 2alive1.94
HCVpro - Hepatitis C Virus Protein Interaction Database South Africa -unstable-
AlzBase - an integrative database for gene dys-regulation in Alzheimer’s disease China 5alive5.00
GTRD - Gene Transcription Regulation Database Russian Federation 0alive0.00
LNCediting United States 0alive0.00
POSTAR - POST-trAnscriptional Regulation China 1alive0.97
RAID - RNA Association Interaction Database China 34alive11.33
SNP2TFBS Switzerland 0alive0.00
mutLBSgeneDB - mutated Ligand Binding Site gene DataBase
United States 1alive1.00
HIPPIE - Human Integrated Protein-Protein Interaction rEference Spain 49alive12.25
pathDIP - Pathway Data Integration Portal
Canada 1alive1.00
XTalkDB
United States 0alive0.00
3DSNP China 0unstable0.00
SoyNet Korea Rep. 0alive0.00
ccNET China 0unstable0.00
DrumPID - drug-minded protein interaction database
Germany 3alive3.00
HPIDB - Host - Pathogen Interaction Database United States 79alive11.06
CCSI - Chromatin–Chromatin Spatial Interaction China 0unstable0.00
ATtRACT
Spain 2unstable1.64
UbiNet - Ubiquitylation Networks Taiwan 1unstable0.95
Abasy Atlas - Across-bacteria systems Atlas Mexico 1alive1.00
DDRprot Spain 2alive0.67
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 3unstable2.85
PathwaysWeb
United States 0alive0.00
PDID - Protein–Drug Interaction Database Canada 2unstable1.88
lnCaNet Australia 6alive6.00
cMapper Korea Rep. 0alive0.00
NaviCom - Connects data to network maps France 12dead0.00
* Citations derived from Google Scholar.
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