|
GO:0006108
|
BP
|
malate metabolic process
|
The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
|
FH,
ME2,
MDH1,
MDH2,
ME3,
MDH1B
|
|
GO:0006110
|
BP
|
regulation of glycolytic process
|
Any process that modulates the frequency, rate or extent of glycolysis.
|
OGT,
PGAM1,
PRKAG1,
EIF6
|
|
GO:0006111
|
BP
|
regulation of gluconeogenesis
|
Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
|
FBP1,
LEP,
VIMP,
NLN,
SDHAF3
|
|
GO:0006112
|
BP
|
energy reserve metabolic process
|
The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
|
MYC,
ADRB3,
MT3,
MC4R,
LEP,
LEPR,
GNAS,
GFPT1,
GNAS,
PID1,
MRAP2,
KL
|
|
GO:0006114
|
BP
|
glycerol biosynthetic process
|
The chemical reactions and pathways resulting in the formation of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
|
LEP
|
|
GO:0006116
|
BP
|
NADH oxidation
|
A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADH, to the oxidized form, NAD.
|
PCK2
|
|
GO:0006117
|
BP
|
acetaldehyde metabolic process
|
The chemical reactions and pathways involving acetaldehyde, a colorless, flammable liquid intermediate in the metabolism of alcohol.
|
RELA
|
|
GO:0006119
|
BP
|
oxidative phosphorylation
|
The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
|
UQCRH,
UQCRB,
UQCRC2,
ATP5D,
UQCRC1,
ATP5C1,
MSH2,
FXN,
CHCHD10,
TEFM
|
|
GO:0006120
|
BP
|
mitochondrial electron transport, NADH to ubiquinone
|
The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex I.
|
NDUFS8,
NDUFA4,
NDUFAB1,
NDUFA1,
NDUFS4,
NDUFA2,
NDUFS2,
NDUFS6,
NDUFB6,
NDUFB4,
NDUFB8,
NDUFA7,
NDUFA10,
NDUFB10,
DLD,
NDUFB7,
NDUFV2,
NDUFS1,
NDUFV3,
NDUFA5,
NDUFA11,
NDUFB11,
NDUFA13
|
|
GO:0006121
|
BP
|
mitochondrial electron transport, succinate to ubiquinone
|
The transfer of electrons from succinate to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex II.
|
SDHC
|
|
GO:0006122
|
BP
|
mitochondrial electron transport, ubiquinol to cytochrome c
|
The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
|
UQCRHL,
UQCRQ,
UQCR11,
PMPCB,
UQCRH,
CYC1,
UQCRB,
UQCRC2,
UQCRC1,
UQCRFS1,
CYCS,
UQCC3,
UQCR10
|
|
GO:0006123
|
BP
|
mitochondrial electron transport, cytochrome c to oxygen
|
The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
|
NDUFA4,
COX6C,
COX5B,
COX6A1,
COX6B1,
COX7C,
COX5A,
COX7B,
CYCS
|
|
GO:0006139
|
BP
|
nucleobase-containing compound metabolic process
|
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
|
TK2,
PNP,
TK1,
TYMS,
PRPS2,
CTPS1,
DUT,
TPMT,
ERH,
MTAP,
DPYSL2,
UPP1,
SLC29A1,
ZNRD1,
SLC23A2,
REXO2
|
|
GO:0006144
|
BP
|
purine nucleobase metabolic process
|
The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
|
ACPP,
GMPR,
PRPS1
|
|
GO:0006145
|
BP
|
purine nucleobase catabolic process
|
The chemical reactions and pathways resulting in the breakdown of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
|
DPYD
|
|
GO:0006148
|
BP
|
inosine catabolic process
|
The chemical reactions and pathways resulting in the breakdown of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs.
|
PNP
|
|
GO:0006154
|
BP
|
adenosine catabolic process
|
The chemical reactions and pathways resulting in the breakdown of adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
|
ADA
|
|
GO:0006157
|
BP
|
deoxyadenosine catabolic process
|
The chemical reactions and pathways resulting in the breakdown of deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA.
|
ADA
|
|
GO:0006163
|
BP
|
purine nucleotide metabolic process
|
The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
|
NME4,
NME1,
NME2,
FHIT,
GUK1
|
|
GO:0006164
|
BP
|
purine nucleotide biosynthetic process
|
The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
|
PFAS,
MTHFD1,
ADSL,
PRPS1,
PPAT,
MTHFD2L
|
|
GO:0006165
|
BP
|
nucleoside diphosphate phosphorylation
|
The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
|
NME4,
NME6,
AK1,
NME1,
NME2,
AK4,
CMPK1,
PCK1,
CMPK2,
AK8,
NME7
|
|
GO:0006166
|
BP
|
purine ribonucleoside salvage
|
Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
|
MTAP
|
|
GO:0006167
|
BP
|
AMP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
|
ADSS,
ADSL,
PRPS1,
ADSSL1
|
|
GO:0006168
|
BP
|
adenine salvage
|
Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
|
APRT
|
|
GO:0006171
|
BP
|
cAMP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
|
ADCY3,
ADCY9,
ADM,
ADCY7
|
|
GO:0006172
|
BP
|
ADP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate.
|
AK1,
AK4,
AK3
|
|
GO:0006177
|
BP
|
GMP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
|
GMPS
|
|
GO:0006182
|
BP
|
cGMP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of cyclic GMP, guanosine 3',5'-phosphate.
|
NPPB,
NPR2,
HTR2C,
HTR2B,
GUCY2D
|
|
GO:0006183
|
BP
|
GTP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
|
NME4,
NME6,
NME1,
NME2,
NME7
|
|
GO:0006185
|
BP
|
dGDP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of dGDP, deoxyguanosine diphosphate, (2'-deoxyguanosine 5'-diphosphate).
|
GUK1
|
|
GO:0006189
|
BP
|
de novo' IMP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
|
PFAS,
GART,
PAICS,
ADSL,
PPAT
|
|
GO:0006195
|
BP
|
purine nucleotide catabolic process
|
The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
|
PNP,
GPX1,
NT5E,
NUDT1,
XDH,
NT5C,
NUDT15
|
|
GO:0006196
|
BP
|
AMP catabolic process
|
The chemical reactions and pathways resulting in the breakdown of AMP, adenosine monophosphate.
|
NT5E,
AMPD3
|
|
GO:0006198
|
BP
|
cAMP catabolic process
|
The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
|
PDE8A,
PDE8B,
PDE4C,
PDE4D,
PDE3B,
PDE7A,
PDE3A,
PDE7B
|
|
GO:0006203
|
BP
|
dGTP catabolic process
|
The chemical reactions and pathways resulting in the breakdown of dGTP, guanosine triphosphate.
|
NUDT1,
NUDT15,
SAMHD1
|
|
GO:0006206
|
BP
|
pyrimidine nucleobase metabolic process
|
The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
|
TYMP,
RRM1,
UPRT,
UCK2,
UCK1,
UCKL1
|
|
GO:0006207
|
BP
|
de novo' pyrimidine nucleobase biosynthetic process
|
The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
|
UMPS,
CAD,
CMPK1,
DHODH
|
|
GO:0006208
|
BP
|
pyrimidine nucleobase catabolic process
|
The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
|
DPYD
|
|
GO:0006210
|
BP
|
thymine catabolic process
|
The chemical reactions and pathways resulting in the breakdown of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base.
|
ALDH6A1,
DPYD
|
|
GO:0006212
|
BP
|
uracil catabolic process
|
The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.
|
DPYD
|
|
GO:0006213
|
BP
|
pyrimidine nucleoside metabolic process
|
The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
|
ERH
|
|
GO:0006214
|
BP
|
thymidine catabolic process
|
The chemical reactions and pathways resulting in the breakdown of thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA.
|
DPYD
|
|
GO:0006218
|
BP
|
uridine catabolic process
|
The chemical reactions and pathways resulting in the breakdown of uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids.
|
UPP1
|
|
GO:0006220
|
BP
|
pyrimidine nucleotide metabolic process
|
The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
|
NME4,
NME1,
NME2,
DCK,
DCTD,
CTPS2
|
|
GO:0006221
|
BP
|
pyrimidine nucleotide biosynthetic process
|
The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
|
PRPS1,
ERH
|
|
GO:0006222
|
BP
|
UMP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.
|
UMPS,
CMPK1,
UPRT
|
|
GO:0006226
|
BP
|
dUMP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
|
DUT
|
|
GO:0006227
|
BP
|
dUDP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).
|
DTYMK,
CMPK2
|
|
GO:0006228
|
BP
|
UTP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
|
NME4,
NME6,
NME1,
NME2,
CAD,
NME7
|
|
GO:0006231
|
BP
|
dTMP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
|
TYMS,
SHMT1
|
|
GO:0006233
|
BP
|
dTDP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
|
DTYMK,
CMPK2
|
|
GO:0006235
|
BP
|
dTTP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
|
TYMS,
DTYMK,
CMPK2
|
|
GO:0006238
|
BP
|
CMP salvage
|
Any process that generates CMP, cytidine monophosphate, from derivatives of it without de novo synthesis.
|
UCK2
|
|
GO:0006241
|
BP
|
CTP biosynthetic process
|
The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
|
NME4,
NME6,
NME1,
CTPS1,
NME2,
NME7
|
|
GO:0006258
|
BP
|
UDP-glucose catabolic process
|
The chemical reactions and pathways resulting in the breakdown of UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate.
|
GALT
|
|
GO:0006259
|
BP
|
DNA metabolic process
|
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
|
TK1,
NME1,
LIG1,
NT5E,
IGFBP4,
ADRA1D,
MKI67,
KPNA2,
POLG,
TOPBP1,
TREX2
|
|
GO:0006260
|
BP
|
DNA replication
|
The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
|
CDC7,
NFIB,
CHEK1,
ORC5,
RAD1,
NBN,
RNASEH2A,
RECQL4,
IGF1,
CDK1,
NFIC,
POLA1,
TOP1,
PTMS,
RRM1,
CDK2,
MCM3,
POLD1,
RBMS1,
CDC25A,
CDC25C,
RRM2,
DUT,
MCM4,
MCM5,
MCM7,
RPA3,
RFC4,
RFC2,
BRCA1,
FEN1,
RFC5,
RFC3,
NASP,
MCM2,
MRE11A,
DNA2,
BLM,
NAP1L1,
POLE2,
SET,
SSBP1,
POLE,
SSRP1,
RBBP4,
CHAF1A,
CHAF1B,
ORC1,
POLA2,
MCM6,
KIAA0101,
CCDC88A,
TBRG1,
RAD9B,
NOL8,
MCM10,
RBBP6,
INO80E,
CHTF18,
ATRIP,
KCTD13,
TOPBP1,
RAD50,
RAD9A,
BARD1,
CDC6,
RHNO1,
DSCC1,
TIPIN,
REPIN1,
CDT1,
POLD4,
POLE3,
DTL,
ORC3,
POLK,
DBF4,
MCM8,
POLI,
TIMELESS,
EXO1,
POLH,
SUPT16H,
ORC6
|
|
GO:0006261
|
BP
|
DNA-dependent DNA replication
|
A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
|
CDK2AP1,
REV3L,
POLQ,
POLG,
POLE2,
TFAM,
POLD4,
BAZ1A
|
|
GO:0006264
|
BP
|
mitochondrial DNA replication
|
The process in which new strands of DNA are synthesized in the mitochondrion.
|
DNA2,
POLG,
PRIMPOL,
PEO1,
MGME1
|
|
GO:0006265
|
BP
|
DNA topological change
|
The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
|
HMGB1,
TOP1,
TOP2A,
HMGB2
|
|
GO:0006266
|
BP
|
DNA ligation
|
The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
|
TOP2A
|
|
GO:0006267
|
BP
|
pre-replicative complex assembly involved in nuclear cell cycle DNA replication
|
The aggregation, arrangement and bonding together of a set of components to form the nuclear pre-replicative complex, a protein-DNA complex that forms at the eukaryotic DNA replication origin and is required for replication initiation.
|
ORC3
|
|
GO:0006268
|
BP
|
DNA unwinding involved in DNA replication
|
The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
|
TOP2A,
HMGA1,
MCM4,
MCM7,
MCM2,
PURA,
RAD51,
MCM6,
PEO1
|
|
GO:0006269
|
BP
|
DNA replication, synthesis of RNA primer
|
The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
|
POLA1,
PRIM1,
PRIM2,
PRIMPOL
|
|
GO:0006270
|
BP
|
DNA replication initiation
|
The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
|
CDC7,
ORC5,
CCNE2,
POLA1,
MCM3,
MCM4,
MCM5,
MCM7,
CDC34,
PRIM1,
PRIM2,
MCM2,
POLE2,
PURA,
POLE,
ORC1,
POLA2,
MCM6,
MCM10,
TOPBP1,
CDC6,
SLF1,
GINS4,
ORC3,
LRWD1,
ORC6
|
|
GO:0006271
|
BP
|
DNA strand elongation involved in DNA replication
|
The process in which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
|
POLA1,
PCNA,
POLD1,
RFC4,
RFC3,
PRIM1,
PRIM2,
POLA2,
GINS1,
POLD3,
GINS4,
GINS3,
POLD4,
GINS2
|
|
GO:0006272
|
BP
|
leading strand elongation
|
The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork.
|
POLA1,
PCNA
|
|
GO:0006273
|
BP
|
lagging strand elongation
|
The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork.
|
PARP1,
POLA1,
PARP2
|
|
GO:0006275
|
BP
|
regulation of DNA replication
|
Any process that modulates the frequency, rate or extent of DNA replication.
|
PPP2R1A,
ID3,
CCDC88A,
ESCO2,
RBBP6,
ZBTB38,
EHMT2,
DSCC1,
NUCKS1,
SMC3
|
|
GO:0006278
|
BP
|
RNA-dependent DNA biosynthetic process
|
A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
|
PPIA,
PTGES3,
TEP1
|
|
GO:0006281
|
BP
|
DNA repair
|
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
|
EYA2,
CHEK1,
BACH1,
FANCG,
RAD51C,
RAD1,
CDC14B,
POLQ,
RAD51D,
RECQL4,
UBR5,
MBD4,
EYA4,
PTTG1,
ACTL6A,
CDK1,
NPM1,
ERCC1,
PARP1,
UNG,
LIG1,
MSH3,
GADD45A,
CDK2,
POLD1,
GTF2H1,
NUDT1,
FEN1,
RFC5,
MSH2,
RECQL,
ATRX,
CSNK1D,
UBE2A,
CSNK1E,
MRE11A,
MSH6,
BLM,
VCP,
POLE2,
UBE2D3,
UBE2B,
BTG2,
XPC,
RAD51,
FOXM1,
SSRP1,
CHAF1A,
CHAF1B,
TRIM28,
ALKBH1,
SMC1A,
KIF22,
PSME4,
SHPRH,
MORF4L2,
NONO,
PDS5A,
EPC2,
INO80D,
ERCC6L2,
INTS3,
NFRKB,
RFWD3,
INO80C,
RAD9B,
USP45,
RPS27L,
EMSY,
CHD1L,
SLF2,
EID3,
APITD1,
JMY,
INO80E,
BOD1L1,
TOPBP1,
RAD54L,
GTF2H4,
RAD50,
ERCC4,
NABP1,
RAD51AP1,
UBE2W,
OTUB1,
SMG1,
USP28,
UHRF1,
CDC5L,
RAD9A,
NABP2,
TREX2,
SLF1,
PAGR1,
TEX15,
FANCD2,
INO80B,
TAOK3,
PIF1,
UBE2T,
INIP,
RAD18,
PDS5B,
TDP1,
PARPBP,
NSMCE4A,
BCCIP,
POLK,
PARP2,
MUTYH,
FZR1,
POLI,
STUB1,
EXO1,
SMC3,
RUVBL2,
POLH,
RUVBL1,
ASF1A,
FAN1,
TRRAP,
SUPT16H,
UCHL5
|
|
GO:0006282
|
BP
|
regulation of DNA repair
|
Any process that modulates the frequency, rate or extent of DNA repair.
|
USP1,
UBE2V1,
UBE2V2,
POLH
|
|
GO:0006283
|
BP
|
transcription-coupled nucleotide-excision repair
|
The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
|
POLR2D,
ERCC1,
UBC,
PCNA,
ERCC2,
LIG1,
POLR2E,
XPA,
POLR2A,
POLD1,
POLR2B,
GTF2H1,
RPA3,
RFC4,
RFC2,
POLR2I,
RFC5,
RFC3,
CDK7,
POLR2J,
POLR2K,
POLR2G,
POLR2L,
RBX1,
RPS27A,
UBA52,
EP300,
CUL4A,
CUL4B,
GTF2H2,
POLD3,
COPS6,
GTF2H4,
ERCC4,
COPS8,
COPS7B,
POLD4,
POLK,
PRPF19,
PPIE
|
|
GO:0006284
|
BP
|
base-excision repair
|
In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
|
POLQ,
RECQL4,
TP53,
UNG,
LIG1,
XPA,
MPG,
RPA3,
FEN1,
DNA2,
HMGA2,
TDG,
SMUG1,
HUWE1,
NEIL3,
PRMT6,
PARP2
|
|
GO:0006285
|
BP
|
base-excision repair, AP site formation
|
The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
|
NTHL1,
TDG
|
|
GO:0006287
|
BP
|
base-excision repair, gap-filling
|
Repair of the damaged strand by the combined action of an apurinic endouclease that degrades a few bases on the damaged strand and a polymerase that synthesizes a 'patch' in the 5' to 3' direction, using the undamaged strand as a template.
|
POLD1,
POLG,
POLE
|
|
GO:0006289
|
BP
|
nucleotide-excision repair
|
A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
|
RAD51D,
TP53,
ERCC1,
ERCC2,
RPA3,
BRCA2,
ATXN3,
RAD23A,
RAD23B,
XPC,
GTF2H2C_2,
SLC30A9,
NEIL3,
GTF2H4,
ERCC4,
FAN1
|
|
GO:0006290
|
BP
|
pyrimidine dimer repair
|
The repair of UV-induced T-T, C-T and C-C dimers.
|
POLH
|
|
GO:0006293
|
BP
|
nucleotide-excision repair, preincision complex stabilization
|
The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
|
ERCC1,
PARP1,
ERCC2,
XPA,
GTF2H1,
RPA3,
RBX1,
CUL4A,
CUL4B,
GTF2H2,
CHD1L,
GTF2H4,
ERCC4
|
|
GO:0006294
|
BP
|
nucleotide-excision repair, preincision complex assembly
|
The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
|
PARP1,
UBC,
ERCC2,
XPA,
GTF2H1,
RPA3,
CDK7,
RAD23B,
RBX1,
RPS27A,
UBA52,
XPC,
CUL4A,
CUL4B,
GTF2H2,
CHD1L,
GTF2H4
|
|
GO:0006295
|
BP
|
nucleotide-excision repair, DNA incision, 3'-to lesion
|
The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
|
ERCC1,
PARP1,
ERCC2,
XPA,
GTF2H1,
RPA3,
RBX1,
CUL4A,
CUL4B,
GTF2H2,
CHD1L,
GTF2H4,
ERCC4
|
|
GO:0006296
|
BP
|
nucleotide-excision repair, DNA incision, 5'-to lesion
|
The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
|
ERCC1,
PARP1,
UBC,
PCNA,
ERCC2,
XPA,
POLD1,
GTF2H1,
RPA3,
RFC4,
RFC2,
RFC5,
RFC3,
RBX1,
RPS27A,
UBA52,
NTHL1,
CUL4A,
CUL4B,
GTF2H2,
POLD3,
CHD1L,
GTF2H4,
ERCC4,
POLD4,
POLK
|
|
GO:0006297
|
BP
|
nucleotide-excision repair, DNA gap filling
|
Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
|
UBC,
PCNA,
LIG1,
POLD1,
RPA3,
RFC4,
RFC2,
RFC5,
RFC3,
RPS27A,
UBA52,
POLE,
POLD3,
POLD4,
POLK
|
|
GO:0006298
|
BP
|
mismatch repair
|
A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
|
RNASEH2A,
PCNA,
LIG1,
MSH3,
POLD1,
RPA3,
MLH1,
MSH2,
MSH6,
PMS1,
XPC,
TDG,
POLD3,
POLD4,
MLH3,
MUTYH,
EXO1
|
|
GO:0006301
|
BP
|
postreplication repair
|
The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
|
BRCA1,
MSH2,
UBE2A,
UBE2B,
UBE2V1,
UBE2V2,
RAD18
|
|
GO:0006302
|
BP
|
double-strand break repair
|
The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
|
MEIOC,
EME2,
APBB1,
BACH1,
RAD21,
SMARCA5,
NBN,
POLQ,
RNF8,
RECQL4,
TDP2,
ERCC1,
PARP1,
XRCC5,
H2AFX,
BRCA1,
FEN1,
MSH2,
BRCC3,
MRE11A,
BRCA2,
VCP,
PRKDC,
MTA1,
XRCC4,
TRIP13,
ESCO2,
SETX,
RAD50,
EME1,
CDCA5,
CIB1,
MND1,
TDP1,
BAZ1B,
KIAA0430
|
|
GO:0006303
|
BP
|
double-strand break repair via nonhomologous end joining
|
The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
|
NBN,
RNF8,
WHSC1,
POLA1,
XRCC5,
H2AFX,
BRCA1,
MLH1,
BRCC3,
MRE11A,
HIST1H4A,
PRKDC,
XRCC4,
MDC1,
UBE2V2,
RIF1,
RAD50,
DCLRE1C,
BARD1,
PRPF19,
KDM2A,
XRCC6BP1
|
|
GO:0006306
|
BP
|
DNA methylation
|
The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
|
FOS,
DNMT1,
ATRX,
GNAS,
EZH2,
GNAS,
ATF7IP,
GATAD2A,
KMT2E,
EHMT2,
DNMT3B
|
|
GO:0006307
|
BP
|
DNA dealkylation involved in DNA repair
|
The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
|
MPG,
ALKBH1,
ASCC3,
FTO,
ASCC2
|
|
GO:0006308
|
BP
|
DNA catabolic process
|
The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
|
AIFM1,
TATDN1
|
|
GO:0006309
|
BP
|
apoptotic DNA fragmentation
|
The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
|
DFFA,
HMGB1,
HMGB2,
KPNA1,
FOXL2,
KPNB1,
DICER1
|
|
GO:0006310
|
BP
|
DNA recombination
|
Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
|
BACH1,
HMGB3,
RAD51C,
RAD21,
RECQL4,
ACTL6A,
ERCC1,
HMGB1,
XRCC5,
RAG1,
ATRX,
MRE11A,
BLM,
RAD51,
XRCC4,
NONO,
TSN,
INO80D,
NFRKB,
INO80C,
SETX,
SUPV3L1,
EID3,
INO80E,
RAD54L,
RAD50,
PAGR1,
INO80B,
PIF1,
NSMCE4A,
PSMC3IP,
EXO1,
RUVBL2,
RUVBL1,
UCHL5
|
|
GO:0006311
|
BP
|
meiotic gene conversion
|
The cell cycle process in which genetic information is transferred from one helix to another. It often occurs in association with general genetic recombination events, and is believed to be a straightforward consequence of the mechanisms of general recombination and DNA repair. For example, meiosis might yield three copies of the maternal version of an allele and only one copy of the paternal allele, indicating that one of the two copies of the paternal allele has been changed to a copy of the maternal allele.
|
MSH2
|
|
GO:0006312
|
BP
|
mitotic recombination
|
The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles.
|
RAD51C,
RAD51D,
FSBP,
ERCC1,
TOP2A,
RAD51,
APITD1,
RAD54B
|
|
GO:0006323
|
BP
|
DNA packaging
|
Any process in which DNA and associated proteins are formed into a compact, orderly structure.
|
KAT6A,
ASH1L
|
|
GO:0006325
|
BP
|
chromatin organization
|
Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
|
HDAC3,
SOX15,
HMGB2,
HMGA2,
SATB1,
HDAC1,
TAF5,
EZH2,
SETD7,
ZNF462,
HDAC8,
NUCKS1,
SMARCAD1,
TCF7L1,
HMG20A,
LRWD1,
PADI4,
HDAC5,
L3MBTL1,
LAS1L
|
|
GO:0006333
|
BP
|
chromatin assembly or disassembly
|
The formation or destruction of chromatin structures.
|
HIRIP3,
HDAC8,
SUV39H2,
BAZ1B
|
|
GO:0006334
|
BP
|
nucleosome assembly
|
The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
|
SMARCA5,
HIST1H2BK,
H2AFY,
NPM1,
HIST1H1E,
H2AFX,
HIST1H1C,
BRD2,
HMGB2,
HIST1H2BB,
ATRX,
SOX9,
CENPA,
MCM2,
NAP1L1,
HIST1H2BD,
HIST1H4A,
HIST1H2BC,
HIST1H3D,
H3F3A,
SET,
HIST1H1A,
SHPRH,
SART3,
HIST2H2BE,
SPTY2D1,
TSPYL5,
KAT6B,
H1FX,
ANP32B,
KAT6A,
HIST1H2BH,
NAP1L5,
RSF1,
NAP1L3,
NAP1L4,
ANP32E,
TSPYL2,
SMYD3,
NAA60,
H2AFY2,
TSPYL4,
NAP1L2,
PADI4,
ASF1A
|
|
GO:0006335
|
BP
|
DNA replication-dependent nucleosome assembly
|
The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
|
NASP,
HIST1H4A,
HIST1H3D,
RBBP4,
CHAF1A,
CHAF1B,
IPO4,
ASF1B,
ASF1A
|
|
GO:0006336
|
BP
|
DNA replication-independent nucleosome assembly
|
The formation of nucleosomes outside the context of DNA replication.
|
ATRX,
NASP,
HIRA,
HIST1H4A,
H3F3A,
RBBP4,
IPO4,
ASF1B,
ASF1A,
CABIN1
|