Molecular Biology International / 2011 / Article / Tab 1

Review Article

Databases and Bioinformatics Tools for the Study of DNA Repair

Table 1

Databases dedicated to DNA repair and general-purpose databases relevant to DNA repair.


Databases dedicated to DNA repair

REPAIRtoire[22]Database of DNA repair pathways
repairGENES of DNA repair genes
Human DNA Repair Genes[17]Database of human DNA repair genes
Repair-FunMapcurrently unavailable[23]A database of interactions between proteins involved in DNA repair and other proteins

Other databases relevant to DNA repair

KEGG[21]Kyoto Encyclopedia of Genes and Genomes
Reactome[24]Database of human pathways and reactions
GeneSNPs Environmental Genome Project web resource integrates gene, sequence, and polymorphism data into individually annotated gene models. The human genes included are related to DNA repair, cell cycle control, cell signaling, cell division, homeostasis, and metabolism
Mouse Mutation Database[25]The Database of mouse strains carrying targeted mutations in genes affecting cellular responses to DNA damage
BioCyc (EcoCyc, MetaCyc) [26]Experimentally studied metabolic pathways and enzymes from more than 1,500 organisms
BRENDA[27]The main collection of enzyme functional data
Pathway Commons[28]A collection of publicly available pathway data from multiple organisms
NGSethDB[29]Database for next-generation sequencing single-cytosine-resolution DNA methylation data
DNAreplication[30]Database for the eukaryotic DNA replication community
MethyCancer[31]Links between DNA methylation levels and cancer
PubMeth[32]Links between DNA methylation levels and cancer
MethDB (2009)[33]The database for DNA methylation and environmental epigenetic effects
OriDB[34]Confirmed and predicted DNA replication origin sites
REBASE[35]Enzymes and genes for DNA restriction and modification in prokaryotes
ROSPath[36]Reactive oxygen species (ROS) signaling pathway proteins
Pathguide[37]A listing of pathway, signal transduction, and protein-protein interaction databases
CREMOFAC[38]Chromatin remodeling factors
DAnCER[39]Disease-Annotated Chromatin Epigenetics Resource
Telomerase database[40]Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components
Replication Domain[41]Replication timing database and genome-wide data visualization tool

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