Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
COXPRESdb - Coexpression Database Japan 230alive23.00
miRDB - miRNA target prediction and functional annotations database United States 465alive46.50
lncRNAdb Australia 351alive49.64
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
RGD - Rat Genome Database United States 60unstable15.00
Open TG-GATEs - Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System Japan 17dead0.00
miRTarBase - miRNA Target Database Taiwan 899alive128.43
NONCODE - Noncoding RNAs China 637unstable35.28
TFBSshape - DNA shape features of transcription factor binding sites United States 39unstable8.97
Hemolytik - Database of Hemolytic peptides India 13alive3.25
Reactome - A Curated Pathway Database United States 615unstable103.01
MitoBreak - The mitochondrial DNA breakpoints database Portugal 4alive0.98
APPRIS - Annotating Principal Splice Isoforms Spain 39alive7.80
TSGene - tumor suppressor gene database United States 89unstable3.20
HAGR - Human Ageing Genomic Resources United Kingdom 595alive45.77
SpermatogenesisOnline - Annotation of Genes/Proteins Involved in Spermatogenesis China 7dead0.00
IntAct United Kingdom 499unstable54.06
PINA - Protein Interaction Network Analysis Australia 281unstable24.35
KaPPA-View4 - Kazusa Plant Pathway Viewer Japan 36alive5.14
HitPredict Japan 57alive8.14
GATMD - GABA Transporter Mutagenesis Database United States 7dead0.00
EuroDia - EuroDia MicroArray Database Switzerland 9dead0.00
GermOnline - GermOnline France 63unstable4.10
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.24
CARLSBAD United States 5alive0.98
Nencki Genomics Database - Ensembl Funcgen Enhanced With Intersections, User Data and Genome-wide TFBS Motifs. Poland 5unstable0.82
miRBase Tracker - miRBase Tracker Belgium 14unstable3.29
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 8unstable1.50
miRGate - miRGate Spain 3unstable0.87
LMPID - Linear Motif mediated Protein Protein Interaction Database India 1alive0.33
CBN - Causal biological network database Switzerland 7alive2.24
NeuroPedia - Neuropeptide Database United States 15alive2.10
PEpiD - Prostate Epigenetic Database China 5unstable0.80
SyStemCell China 6unstable0.58
C-It Germany 11alive1.36
TiSGeD - Tissue-Specific Genes Database China 64unstable7.44
MPID-T2 - MHC-Peptide Interaction Database-TR version 2 Australia 8unstable0.77
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
NPRD - Nucleosome Positioning Region Database Russian Federation 20alive1.52
ECgene - ECgene Korea Rep. 167unstable6.29
TRED - Transcriptional Regulatory Element Database United States 155alive11.57
PolyA_DB United States 83alive6.38
SPD - Secreted Protein Database China 119unstable4.03
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
RatMap - rat genome information Sweden 13unstable0.70
DG-CST - Disease Gene Conserved Sequence Tags Database Italy 17alive1.29
ABS - database of Annotated regulatory Binding Sites from orthologous promoters Spain 68alive5.67
cisRED - cisRED Canada 112unstable7.19
DBD - Transcription factor prediction database United Kingdom 156unstable12.22
Argonaute Germany 88alive7.33
miRNAMap - A database of experimentally verified microRNAs and miRNA target genes Taiwan 359alive29.32
RNAi Codex United States 48alive4.00
UCbase & miRfunc - Ultraconserved sequences data and miRNA function United States 58dead0.00
Degradome - The Degradome database Spain 107dead0.00
PIG - Pathogen Interaction Gateway United States 55unstable1.16
ExDom - ExDom United States 10unstable0.23
ERGR - ethanol-related gene resource United States 32dead0.00
microRNA.org - microRNA.org-Targets and Expression United States 1199unstable95.92
piRNABank - A web resource on classified and clustered Piwi-interacting RNAs India 111unstable10.43
Vir-Mir - The viral miRNA prediction database Taiwan 60alive5.88
Greglist - Database of G-quadruplex Regulated Genes China 43unstable2.75
SNPSTR - microsatellite marker and tightly linked SNPs United Kingdom 31alive2.73
GAN - Gene Aging Nexus United States 38unstable1.04
QTL MatchMaker United States 5unstable0.34
GenBank - GenBank United States 46415unstable492.28
piRNA cluster db - piRNA cluster database Germany 29unstable4.49
iGNM - Gaussian Network Model Database United States 116alive8.92
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
IID - Integrated interactions database Canada 1alive0.50
piRNAQuest - searching the piRNAome for silencers India 4alive0.99
MTD - mammalian transcriptomic database China 0alive0.00
R-loopDB Singapore 0alive0.00
WERAM - Writers, Erasers and Readers of Acetylation & Methylation China 1alive1.00
SinEx DB - SinEx DATABASE Chile 0alive0.00
Tfcheckpoint - Transcription Factor Checkpoint Norway 8alive1.60
RAIN - RNA–protein Association and Interaction Networks Switzerland 3unstable0.99
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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