Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation United States 363alive40.33
MoonProt - Moonlighting Proteins Database United States 20alive6.47
RCSB PDB - RCSB Protein Data Bank United States 853unstable69.46
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
CeCaFDB - Central Carbon Metabolic Flux Database China 0unstable0.00
Cyclebase - Cell-cycle Database Denmark 105unstable6.72
MOPED - Multi-Omics Profiling Expression Database United States 5dead0.03
NONCODE - Noncoding RNAs China 637unstable35.28
YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking Portugal 793alive65.42
UniHI - Unified Human Interactome Portugal 194alive17.64
Reactome - A Curated Pathway Database United States 615unstable103.01
SGD - Saccharomyces Genome Database United States 772alive128.67
LoQAtE - The localization and quantitation atlas of the yeast proteome Israel 8unstable1.90
YeastNet - Probabilistic Functional Gene Network of Saccharomyces cerevisiae Korea Rep. 17unstable3.31
Spliceosome Database United States 20alive3.88
SwissRegulon - A Database of Genome-wide Annotations of Regulatory Sites Switzerland 118unstable5.15
MODOMICS - A Database of RNA Modifications Poland 509alive41.99
RNApathwaysDB - RNA Pathways Database Poland 5alive0.99
NetwoRx - Connecting Drugs to Networks and Phenotypes in Saccharomyces Cerevisiae Canada 6alive1.19
PrePPI - A structure-informed database of protein-protein interactions United States 301unstable13.04
HAGR - Human Ageing Genomic Resources United Kingdom 595alive45.77
ScerTF - Saccharomyces cerevisia Transcription Factors Database United States 35unstable2.27
YeTFaSCo - Yeast Transcription Factor Specificity Compendium Canada 31alive5.17
PhenoM - Phenomics of yeast Mutants Canada 196unstable22.30
YMDB - Yeast Metabolome Database Canada 88alive14.37
IntAct United Kingdom 499unstable54.06
PINA - Protein Interaction Network Analysis Australia 281unstable24.35
OGEE - Online GEne Essentiality database China 77alive12.83
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
PHOSIDA - phosphorylation site database Germany 567unstable42.78
IsoBase - IsoRank PPI Network Alignment Based Ortholog Database United States 44alive6.29
RNA helicase database United States 30unstable3.34
YPA - Yeast Promoter Atlas Taiwan 25unstable1.82
HitPredict Japan 57alive8.14
KUPS - University of Kansas Proteomics Service United States 21unstable0.33
REPAIRtoire - A Database of DNA Repair Pathways Poland 24alive3.39
MitoGenesisDB - Mitochondrial Spatio-Temporal Expression Database France 3alive0.42
PhosphoGRID Canada 63unstable2.44
GermOnline - GermOnline France 63unstable4.10
The gene-specific codon counting database - The gene-specific codon counting database United States 8dead0.00
YeastMine - YeastMine United States 54unstable7.56
yApoptosis - yeast apoptosis database Sweden 1alive0.20
GoSynthetic - Synthetic Biology Workbench Germany 2alive0.40
yStreX - Yeast stress expression database Sweden 2alive0.50
HeteroGenome Russian Federation 2unstable0.47
YTRP - Yeast Transcriptional Regulatory Pathway Taiwan 5alive1.23
3DGD - 3D Genome Database China 6unstable0.67
ConsensusPathDB Germany 368unstable28.21
PaGenBase - Pattern Gene Database China 8unstable1.46
YRC PIR - The Yeast Resource Center Public Image Repository United States 20alive2.47
WALTZ-DB - database of amyloid-forming peptides Belgium 0alive0.00
dbGSH - databaseof cysteine S-glutathionylation (GSH) sites Taiwan 25alive6.19
CLIPdb China 0alive0.00
INstruct United States 27alive5.35
NPRD - Nucleosome Positioning Region Database Russian Federation 20alive1.52
Small Subunit rRNA Modification Database United States 62dead0.00
CYGD - Comprehensive Yeast Genome Database Germany 327unstable21.63
PROPHECY - PROfiling of PHEnotypic Characteristics in Yeast Sweden 29alive2.21
YRC PDR - Yeast Resource Center Public Data Repository United States 34alive2.62
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive2.92
DRYGIN - Data Repository of Yeast Genetic Interactions Canada 71alive8.70
Transterm New Zealand 108alive6.55
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable124.58
Genolevures - Genomic Exploration of the Hemiascomycete Yeasts France 223unstable8.28
TransfactomeDB - Yeast Transfactome Database United States 22alive2.18
M3D - Many Microbe Microarrays Database United States 195alive19.50
3D RIBOSOMAL MODIFICATION MAPS DATABASE United States 69alive6.83
OPTIC - Orthologous and Paralogous Transcripts in Clades United Kingdom 32alive3.07
GAN - Gene Aging Nexus United States 38unstable1.04
eSLDB - eSLDB Italy 45alive4.09
MPact - MIPS Protein Interaction Resource on Yeast Germany 357unstable9.22
Genome Snapshot - An Overview Of The Saccharomyces Cerevisiae Genome. United States 85dead0.00
YGOB - Yeast Gene Order Browser Ireland 54alive4.50
PeptideAtlas United States 839alive69.22
MitoP2 - An integrative tool for the analysis of the mitochondrial proteome Germany 156dead0.00
iGNM - Gaussian Network Model Database United States 116alive8.92
SynLethDB Singapore 1unstable0.47
IID - Integrated interactions database Canada 1alive0.50
MethSMRT China 0unstable0.00
R-loopDB Singapore 0alive0.00
RNALocate China 0alive0.00
TFBSbank United Kingdom 0unstable0.00
Membranome - Membrane Proteome United States 1unstable0.61
WERAM - Writers, Erasers and Readers of Acetylation & Methylation China 1alive1.00
ORDB - Olfactory Receptor DataBase United States 71dead0.00
CCSI - Chromatin–Chromatin Spatial Interaction China 0unstable0.00
CoopTFD - Cooperative Transcription Factors Database Taiwan 1alive0.49
RAIN - RNA–protein Association and Interaction Networks Switzerland 3unstable0.99
WikiGenomes United States 0alive0.00
* Citations derived from Google Scholar.
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