Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
ChiTaRS - Chimeric Transcripts and RNA-Sequencing data Israel 48alive9.60
COXPRESdb - Coexpression Database Japan 230alive23.00
EPD - Eukaryotic Promoter Database Switzerland 32alive10.67
Gbshape - Genome Browser Database for DNA Shape Annotations United States 8alive2.67
tRFdb - Transfer RNA related Fragments Database United States 4alive1.31
DIANA-TarBase - DIANA-TarBase Greece 1513alive126.08
lncRNAdb Australia 351alive49.64
InParanoid - ortholog groups with inparalogs Sweden 1253alive95.42
Genome3D - Annotating Genomes with Structures United Kingdom 42unstable4.99
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
FlyBase - Database of Drosophila Genes & Genomes United States 3836alive159.83
SuperFly Spain 0alive0.00
miRBase - microRNA dababase United Kingdom 11326alive792.82
miRTarBase - miRNA Target Database Taiwan 899alive128.43
NONCODE - Noncoding RNAs China 637unstable44.59
NPInter - ncRNA Interaction Database China 119alive9.72
RADAR - Rigorously Annotated Database of A-to-I RNA editing United States 52alive12.87
JASPAR Canada 2924alive204.68
TFBSshape - DNA shape features of transcription factor binding sites United States 39alive9.75
OnTheFly - TF and TFBS On The Fly United States 9unstable0.74
Gene3D - Gene3D United Kingdom 194alive19.40
UniHI - Unified Human Interactome Portugal 194alive17.64
CentrosomeDB Spain 58alive6.19
Reactome - A Curated Pathway Database United States 615unstable132.23
MitoBreak - The mitochondrial DNA breakpoints database Portugal 4alive0.98
Spliceosome Database United States 20alive3.88
ChIPBase China 199unstable23.08
NCBI Epigenomics - NCBI Epigenomics United States 51unstable1.89
Darned - DAtabase of RNa EDiting Ireland 128alive15.84
FlyAtlas - Drosophila gene expression atlas United Kingdom 983alive89.36
H2DB - Heritability Database Annotating with Trait-Associated Genomic Loci Japan 1alive0.20
dbVar - Database of Genomic Structural Variation United States 41unstable3.61
HAGR - Human Ageing Genomic Resources United Kingdom 595alive45.77
SpermatogenesisOnline - Annotation of Genes/Proteins Involved in Spermatogenesis China 7dead0.00
MAPPER2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation United States 116unstable7.23
FlyRNAi - Drosophila RNAi screening center database United States 104unstable7.02
PINA - Protein Interaction Network Analysis Australia 281unstable22.48
OGEE - Online GEne Essentiality database China 77alive12.83
modMine - A Data Warehouse for the modENCODE Project United Kingdom 50unstable7.67
DNAtraffic - DNAtraffic Poland 3unstable0.44
GONUTS - Gene Ontology Normal Usage Tracking System United States 13unstable1.26
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.29
AREsite - AU-rich Elements Site Austria 110alive15.56
FlyFactorSurvey - Database of DNA binding specificities for Drosophila transcription factors (TFs) United States 78alive11.14
REDfly - Regulatory Element Database for Drosophila United States 284alive23.43
PHOSIDA - phosphorylation site database Germany 567unstable48.45
IsoBase - IsoRank PPI Network Alignment Based Ortholog Database United States 44alive6.29
RBPDB - The Database of RNA-binding Protein Specificities Canada 133alive19.00
RNA helicase database United States 30alive4.24
DroID - Drosophila Interactions Database United States 183alive18.30
HitPredict Japan 57alive8.14
KUPS - University of Kansas Proteomics Service United States 21unstable0.45
BrainTrap - Fly Brain Protein Trap Database United Kingdom 14alive1.72
INOH Japan 13dead0.00
modENCODE - The model organism Encyclopedia of DNA Elements United States 18alive2.57
HTS-DB - High-Throughput Screening DataBase United Kingdom 0alive0.00
GoSynthetic - Synthetic Biology Workbench Germany 2alive0.40
miRBase Tracker - miRBase Tracker Belgium 14unstable3.22
miRror-Suite - A dual view on sets of microRNAs and their targets Israel 33alive4.04
HeteroGenome Russian Federation 2unstable0.47
tagtog - tagtog United Kingdom 4alive1.00
3DGD - 3D Genome Database China 6unstable0.86
PaGenBase - Pattern Gene Database China 8unstable1.44
DetoxiProt - An integrated database of detoxification proteins China 3unstable0.34
INstruct United States 27alive5.35
NPRD - Nucleosome Positioning Region Database Russian Federation 20alive1.52
ECgene - ECgene Korea Rep. 167unstable8.22
deepBase - deepBase China 102unstable4.21
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive2.92
FlyTF - Transcription factor datamine for Drosophila melanogaster United Kingdom 128unstable8.96
Transterm New Zealand 108alive6.48
RNAi Codex United States 48alive4.00
MachiBase - A Drosophila Melanogaster 5'-end mRNA Transcription Database. Japan 25alive2.75
miROrtho - The catalogue of animal microRNA genes Switzerland 55alive6.11
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable162.49
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.61
FlyEx - Fly Expression Databse Russian Federation 83unstable7.84
FLYSNPdb - FLYSNPdb Austria 10alive1.11
ERGR - ethanol-related gene resource United States 32dead0.00
TranspoGene - TranspoGene Israel 56alive5.54
microRNA.org - microRNA.org-Targets and Expression United States 1199alive118.70
4DXpress - Expression Database in Four Dimensions Germany 36dead0.00
piRNABank - A web resource on classified and clustered Piwi-interacting RNAs India 111unstable10.21
OPTIC - Orthologous and Paralogous Transcripts in Clades United Kingdom 32unstable3.04
GAN - Gene Aging Nexus United States 38unstable1.31
GeneSpeed - GeneSpeed database United States 10dead0.00
GenBank - GenBank United States 46415unstable632.93
SORFS.ORG Belgium 2alive0.98
SEA - Super-Enhancer Archive China 1alive0.50
FlyVar - fly variation database China 1unstable0.26
SynLethDB Singapore 1unstable0.47
IID - Integrated interactions database Canada 1alive0.50
LNCediting United States 0alive0.00
R-loopDB Singapore 0alive0.00
TFBSbank United Kingdom 0unstable0.00
WERAM - Writers, Erasers and Readers of Acetylation & Methylation China 1alive1.00
Cas-Database Korea Rep. 1alive0.50
SSBD - Systems Science of Biological Dynamics database Japan 7alive2.33
LncVar - genetic variation associated with long non-coding genes China 2alive2.00
* Citations derived from Google Scholar.
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