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.

NameurlReferenceDescription

Databases dedicated to DNA repair

REPAIRtoirehttp://repairtoire.genesilico.pl/[22]Database of DNA repair pathways
repairGENEShttp://www.repairgenes.org/unpublishedDatabase of DNA repair genes
Human DNA Repair Geneshttp://sciencepark.mdanderson.org/labs/wood/DNA_Repair_Genes.html[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

KEGGhttp://www.genome.jp/kegg/[21]Kyoto Encyclopedia of Genes and Genomes
Reactomehttp://www.reactome.org/ReactomeGWT/entrypoint.html[24]Database of human pathways and reactions
GeneSNPshttp://www.genome.utah.edu/genesnps/This 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 Databasehttp://pathcuric1.swmed.edu/research/research.htm[25]The Database of mouse strains carrying targeted mutations in genes affecting cellular responses to DNA damage
BioCyc (EcoCyc, MetaCyc)http://biocyc.org/ [26]Experimentally studied metabolic pathways and enzymes from more than 1,500 organisms
BRENDAhttp://www.brenda-enzymes.org/[27]The main collection of enzyme functional data
Pathway Commonshttp://www.pathwaycommons.org/pc/[28]A collection of publicly available pathway data from multiple organisms
NGSethDBhttp://bioinfo2.ugr.es/NGSmethDB/gbrowse/hg19/[29]Database for next-generation sequencing single-cytosine-resolution DNA methylation data
DNAreplicationhttp://DNAreplication.net/[30]Database for the eukaryotic DNA replication community
MethyCancerhttp://methycancer.psych.ac.cn/[31]Links between DNA methylation levels and cancer
PubMethhttp://matrix.ugent.be/pubmeth/[32]Links between DNA methylation levels and cancer
MethDB (2009)http://www.methdb.de/[33]The database for DNA methylation and environmental epigenetic effects
OriDBhttp://www.oridb.org/index.php[34]Confirmed and predicted DNA replication origin sites
REBASEhttp://rebase.neb.com/rebase/rebase.html[35]Enzymes and genes for DNA restriction and modification in prokaryotes
ROSPathhttp://rospath.ewha.ac.kr/[36]Reactive oxygen species (ROS) signaling pathway proteins
Pathguidehttp://www.pathguide.org/[37]A listing of pathway, signal transduction, and protein-protein interaction databases
CREMOFAChttp://www.jncasr.ac.in/cremofac/[38]Chromatin remodeling factors
DAnCERhttp://wodaklab.org/dancer/[39]Disease-Annotated Chromatin Epigenetics Resource
Telomerase databasehttp://telomerase.asu.edu/[40]Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components
Replication Domainhttp://www.replicationdomain.com/[41]Replication timing database and genome-wide data visualization tool

Article of the Year Award: Outstanding research contributions of 2020, as selected by our Chief Editors. Read the winning articles.