Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
Gbshape - Genome Browser Database for DNA Shape Annotations United States 8alive2.67
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation United States 363alive40.33
tRFdb - Transfer RNA related Fragments Database United States 4alive1.31
DIANA-TarBase - DIANA-TarBase Greece 1513alive126.08
DoRiNA - Database of RNA Interactions in Post-transcriptional Regulation Germany 115alive18.59
InParanoid - ortholog groups with inparalogs Sweden 1253alive95.42
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
Helminth.net United States 12alive4.00
miRTarBase - miRNA Target Database Taiwan 899alive128.43
NONCODE - Noncoding RNAs China 637unstable43.61
NPInter - ncRNA Interaction Database China 119alive9.52
JASPAR Canada 2924alive204.68
TFBSshape - DNA shape features of transcription factor binding sites United States 39alive9.75
UniHI - Unified Human Interactome Portugal 194alive17.64
Reactome - A Curated Pathway Database United States 615unstable127.61
WormQTLHD - A Web Database for Linking Human Disease to Natural Variation Data in C. elegans. Netherlands 27alive5.40
MitoBreak - The mitochondrial DNA breakpoints database Portugal 4alive0.98
Spliceosome Database United States 20alive3.88
ChIPBase China 199unstable23.48
NCBI Epigenomics - NCBI Epigenomics United States 51unstable1.82
WDDD - Worm Developmental Dynamics Database Japan 4alive0.79
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161unstable21.20
HAGR - Human Ageing Genomic Resources United Kingdom 595alive45.77
SpermatogenesisOnline - Annotation of Genes/Proteins Involved in Spermatogenesis China 7dead0.00
Nematode - Nematode.net United States 163alive11.64
PINA - Protein Interaction Network Analysis Australia 281unstable22.79
OGEE - Online GEne Essentiality database China 77alive12.83
modMine - A Data Warehouse for the modENCODE Project United Kingdom 50unstable7.67
DNAtraffic - DNAtraffic Poland 3unstable0.42
GONUTS - Gene Ontology Normal Usage Tracking System United States 13unstable1.21
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.29
AREsite - AU-rich Elements Site Austria 110alive15.56
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 30alive4.16
HitPredict Japan 57alive8.14
KUPS - University of Kansas Proteomics Service United States 21unstable0.42
CPGR - Comprehensive Phytopathogen Genomics Resource United States 10alive1.43
INOH Japan 13dead0.00
modENCODE - The model organism Encyclopedia of DNA Elements United States 18alive2.57
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 2alive0.48
PaGenBase - Pattern Gene Database China 8unstable1.46
dbGSH - databaseof cysteine S-glutathionylation (GSH) sites Taiwan 25alive6.19
DetoxiProt - An integrated database of detoxification proteins China 3unstable0.33
CLIPdb China 0alive0.00
INstruct United States 27alive5.35
deepBase - deepBase China 102unstable4.08
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive2.92
cisRED - cisRED Canada 112unstable6.72
DBD - Transcription factor prediction database United Kingdom 156unstable11.96
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable157.08
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.61
PIG - Pathogen Interaction Gateway United States 55unstable1.47
ERGR - ethanol-related gene resource United States 32dead0.00
UTRome.org - UTRome.org United States 13unstable1.23
CMGSDB - Database for Computational Modeling of Gene Silencing United States 6dead0.00
microRNA.org - microRNA.org-Targets and Expression United States 1199alive118.70
OPTIC - Orthologous and Paralogous Transcripts in Clades United Kingdom 32alive3.07
Greglist - Database of G-quadruplex Regulated Genes China 43unstable2.88
GAN - Gene Aging Nexus United States 38unstable1.28
GeneSpeed - GeneSpeed database United States 10dead0.00
WormBook - the online review of Caenorhabditis elegans biology United States 51alive4.64
eSLDB - eSLDB Italy 45alive4.09
SGCEdb United States 2dead0.00
SEA - Super-Enhancer Archive China 1alive0.50
Digital Development - Digital Development United States 0alive0.00
MethSMRT China 0unstable0.00
TFBSbank United Kingdom 0unstable0.00
WERAM - Writers, Erasers and Readers of Acetylation & Methylation China 1alive1.00
CeNDR - Caenorhabditis elegans Natural Diversity Resource United States 2dead0.00
ORDB - Olfactory Receptor DataBase United States 71dead0.00
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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