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 31unstable9.40
DIANA-TarBase - DIANA-TarBase Greece 1513alive126.08
TopFIND - Termini oriented protein Function Inferred Database Canada 98alive14.00
Genome3D - Annotating Genomes with Structures United Kingdom 42alive5.04
AraNet - Probabilistic Functional Gene Network of Arabidopsis thaliana Korea Rep. 0unstable0.00
Araport - Arabidopsis Information Portal United States 9unstable0.57
CATdb - Complete Arabidopsis Transcriptome database France 0alive0.00
Cyclebase - Cell-cycle Database Denmark 105unstable6.62
NGSmethDB - High-quality Methylation Maps Spain 52unstable5.50
miRBase - microRNA dababase United Kingdom 11326alive792.82
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
Reactome - A Curated Pathway Database United States 615unstable103.01
ppdb - plantpromoterdb Japan 19alive4.70
LSD - Leaf Senescence DataBase China 42unstable5.28
NCBI Epigenomics - NCBI Epigenomics United States 51unstable1.46
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161unstable16.91
MIPS PlantsDB - Plant Genome and Systems Biology Germany 43alive8.60
PhosPhAt - The Arabidopsis Protein Phosphorylation Site Database Germany 416alive41.60
SUBA - The SUBcellular localisation Database for Arabidopsis Proteins Australia 168alive33.60
mirEX - MicroRNA Expression Database Poland 16unstable1.68
PINA - Protein Interaction Network Analysis Australia 281unstable24.35
OGEE - Online GEne Essentiality database China 77alive12.83
MetaCrop - Metabolic pathways in crop plants Germany 73alive7.23
GABI-Kat SimpleSearch - GABI-Kat SimpleSearch Germany 206alive13.73
Plantmetabolomics.org United States 86unstable3.98
DNAtraffic - DNAtraffic Poland 3unstable0.34
GONUTS - Gene Ontology Normal Usage Tracking System United States 13unstable0.97
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.29
PmiRKB - Plant microRNA Knowledge Base China 19alive2.69
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable2.97
KaPPA-View4 - Kazusa Plant Pathway Viewer Japan 36alive5.14
HitPredict Japan 57alive8.14
AGRIS - Arabidopsis Gene Regulatory Information Server United States 701unstable41.59
AHD2 - Arabidopsis Hormone Database 2.0 China 60unstable4.33
AtPID - Arabidopsis thaliana Protein Interactome Database China 136unstable11.42
PAIR - Predicted Arabidopsis Interactome Resource China 32unstable1.19
AthaMap - Arabidopsis thaliana Map Germany 275alive19.45
BFGR - Biofuel Feedstock Genomics Resource United States 12alive2.00
AIM - Arabidopsis Interactome Modules Database United States 0unstable0.00
HeteroGenome Russian Federation 2unstable0.47
EpimiR - Database of Curated Mutual Regulation Between epigenetic Modifications and miRNAs China 8unstable1.50
AtmiRNET Taiwan 3alive0.99
PaGenBase - Pattern Gene Database China 8unstable1.46
KNApSAcK-3D - KNApSAcK-3D Japan 11alive2.20
RARGE II - Arabidopsis Genome Encyclopedia Japan 7alive1.73
RiceFOX - Rice Full-length cDNA Over-expressed Arabidopsis Mutant database Japan 41alive5.74
SABRE2 - Systematic consolidation of Arabidopsis and other Botanical REsources Japan 3unstable0.59
ERISdb - ERISdb Poland 7alive1.39
CoP - Co-expressed biological Processes Japan 51alive6.31
EXPath - EXPath Taiwan 2alive0.67
dbGSH - databaseof cysteine S-glutathionylation (GSH) sites Taiwan 25alive6.19
INstruct United States 27alive5.35
DoOP - Database of Orthologous Promoters Hungary 37unstable1.76
deepBase - deepBase China 102unstable3.31
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive2.92
AMPDB - Arabidopsis Mitochondrial Protein Database Australia 68unstable4.97
AtNoPDB - Arabidopsis Nucleolar Protein Database United Kingdom 61alive4.55
ASRP - Arabidopsis Small RNA Project Database United States 293alive21.86
GeneFarm - GeneFarm France 22dead0.00
Transterm New Zealand 108alive6.55
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable124.58
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.64
CleanEST Korea Rep. 14unstable1.42
ExDom - ExDom United States 10unstable0.23
ATTED-II Japan 711alive64.64
TAIR - The Arabidopsis Information Resource United States 768unstable39.94
PlantTribes United States 57unstable4.56
3D RIBOSOMAL MODIFICATION MAPS DATABASE United States 69alive6.83
Vir-Mir - The viral miRNA prediction database Taiwan 60alive5.88
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 45alive4.09
DRASTIC - Database Resource for the Analysis of Signal Transduction in Cells United Kingdom 17unstable0.33
GenBank - GenBank United States 46415unstable492.28
BRAD - Brassica database China 155alive22.14
FLOR-ID - Flowering Interactive Database Belgium 4alive2.00
PlantDHS - A plant DNase I hypersensitive site database United States 3alive1.44
CANTATAdb - A database of long non-coding RNAs in plants Poland 1alive0.50
MethSMRT China 0unstable0.00
Membranome - Membrane Proteome United States 1unstable0.61
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 2alive1.98
FoldAtlas United Kingdom 1alive0.99
* Citations derived from Google Scholar.
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