Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
RNAcentral United Kingdom 31alive15.04
DIANA-TarBase - DIANA-TarBase Greece 1513alive137.55
TopFIND - Termini oriented protein Function Inferred Database Canada 98alive16.33
Genome3D - Annotating Genomes with Structures United Kingdom 42unstable5.64
AraNet - Probabilistic Functional Gene Network of Arabidopsis thaliana Korea Rep. 0alive0.00
Araport - Arabidopsis Information Portal United States 9unstable1.30
CATdb - Complete Arabidopsis Transcriptome database France 0alive0.00
Cyclebase - Cell-cycle Database Denmark 105alive11.20
NGSmethDB - High-quality Methylation Maps Spain 52unstable5.20
miRBase - microRNA dababase United Kingdom 11326alive853.81
miRTarBase - miRNA Target Database Taiwan 899alive149.83
NONCODE - Noncoding RNAs China 637unstable47.77
TFBSshape - DNA shape features of transcription factor binding sites United States 39alive13.00
Reactome - A Curated Pathway Database United States 615alive205.00
ppdb - plantpromoterdb Japan 19alive6.33
LSD - Leaf Senescence DataBase China 42unstable6.16
NCBI Epigenomics - NCBI Epigenomics United States 51unstable2.55
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161alive30.91
MIPS PlantsDB - Plant Genome and Systems Biology Germany 43alive10.75
PhosPhAt - The Arabidopsis Protein Phosphorylation Site Database Germany 416alive46.22
SUBA - The SUBcellular localisation Database for Arabidopsis Proteins Australia 168alive42.00
mirEX - MicroRNA Expression Database Poland 16unstable2.34
PINA - Protein Interaction Network Analysis Australia 281unstable23.53
OGEE - Online GEne Essentiality database China 77alive15.40
MetaCrop - Metabolic pathways in crop plants Germany 73alive8.03
GABI-Kat SimpleSearch - GABI-Kat SimpleSearch Germany 206alive14.71
Plantmetabolomics.org United States 86unstable6.88
DNAtraffic - DNAtraffic Poland 3unstable0.52
GONUTS - Gene Ontology Normal Usage Tracking System United States 13unstable1.77
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.69
PmiRKB - Plant microRNA Knowledge Base China 19alive3.10
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable3.03
KaPPA-View4 - Kazusa Plant Pathway Viewer Japan 36alive6.00
HitPredict Japan 57alive9.50
AGRIS - Arabidopsis Gene Regulatory Information Server United States 701alive50.07
AHD2 - Arabidopsis Hormone Database 2.0 China 60unstable4.05
AtPID - Arabidopsis thaliana Protein Interactome Database China 136alive14.51
PAIR - Predicted Arabidopsis Interactome Resource China 32unstable1.17
AthaMap - Arabidopsis thaliana Map Germany 275alive20.94
BFGR - Biofuel Feedstock Genomics Resource United States 12alive2.40
AIM - Arabidopsis Interactome Modules Database United States 0unstable0.00
HeteroGenome Russian Federation 2unstable0.63
EpimiR - Database of Curated Mutual Regulation Between epigenetic Modifications and miRNAs China 8unstable1.73
AtmiRNET Taiwan 3alive1.49
PaGenBase - Pattern Gene Database China 8unstable1.80
KNApSAcK-3D - KNApSAcK-3D Japan 11alive2.75
RARGE II - Arabidopsis Genome Encyclopedia Japan 7alive2.33
RiceFOX - Rice Full-length cDNA Over-expressed Arabidopsis Mutant database Japan 41alive6.70
SABRE2 - Systematic consolidation of Arabidopsis and other Botanical REsources Japan 3alive1.00
ERISdb - ERISdb Poland 7alive1.73
CoP - Co-expressed biological Processes Japan 51alive7.29
EXPath - EXPath Taiwan 2alive1.00
dbGSH - databaseof cysteine S-glutathionylation (GSH) sites Taiwan 25alive8.25
INstruct United States 27alive6.68
DoOP - Database of Orthologous Promoters Hungary 37unstable2.90
deepBase - deepBase China 102unstable5.68
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive3.17
AMPDB - Arabidopsis Mitochondrial Protein Database Australia 68alive5.67
AtNoPDB - Arabidopsis Nucleolar Protein Database United Kingdom 61unstable4.83
ASRP - Arabidopsis Small RNA Project Database United States 293alive24.42
GeneFarm - GeneFarm France 22dead0.00
Transterm New Zealand 108alive6.91
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable204.16
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.94
CleanEST Korea Rep. 14alive1.73
ExDom - ExDom United States 10unstable0.39
ATTED-II Japan 711alive71.10
TAIR - The Arabidopsis Information Resource United States 768unstable67.41
PlantTribes United States 57alive6.14
3D RIBOSOMAL MODIFICATION MAPS DATABASE United States 69alive7.59
Vir-Mir - The viral miRNA prediction database Taiwan 60alive6.47
POGs/PlantRBP - POGs/PlantRBP United States 31dead0.00
PlantQTL-GE - A database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information China 21dead0.00
eSLDB - eSLDB Italy 45alive4.50
DRASTIC - Database Resource for the Analysis of Signal Transduction in Cells United Kingdom 17unstable0.54
GenBank - GenBank United States 46415unstable754.24
BRAD - Brassica database China 155alive25.57
FLOR-ID - Flowering Interactive Database Belgium 4alive4.00
PlantDHS - A plant DNase I hypersensitive site database United States 3unstable2.85
CANTATAdb - A database of long non-coding RNAs in plants Poland 1alive0.99
MethSMRT China 0unstable0.00
Membranome - Membrane Proteome United States 1unstable0.59
WERAM - Writers, Erasers and Readers of Acetylation & Methylation China 1alive1.00
AraPheno Germany 0unstable0.00
LncVar - genetic variation associated with long non-coding genes China 2alive2.00
FoldAtlas United Kingdom 1alive1.00
* Citations derived from Google Scholar.
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