CoP: Co-expressed Biological Processes

Biological process to genes

Query process ID GO:0006281

Process name 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.

Organism Oryza sativa

Click Gene ID to show a list of co-expressed genes.

ECC Gene ID Repr. ID Gene name Functional description Ev AGI code Arabidopsis gene name O.I. H.G. Other DB
S Os11g0146800 AB079874.1 - RecA bacterial DNA recombination protein familyprotein 3e-49 At3g22880 DMC1 (DISRUPTION OF MEIOTIC CONTROL 1) O.I. H.G.
S Os12g0143800 AB079873.1 - Meiotic recombination protein DMC1 homolog 7e-38 At3g22880 DMC1 (DISRUPTION OF MEIOTIC CONTROL 1) O.I. H.G.
C Os10g0518900 AK070764.1 - DNA repair protein rad10 family protein 2e-1 At4g01050 hydroxyproline-rich glycoprotein family protein O.I. H.G.
C Os11g0615800 AB080262.1 - RAD51 homolog RAD51A 1e-73 At5g20850 ATRAD51 O.I. H.G.
C Os12g0497300 AB080264.1 - RAD51 homolog RAD51B 7e-75 At5g20850 ATRAD51 O.I. H.G.
L Os01g0180600 NM_189554.1 - MutS homolog 7 (Fragment) 1e-10 At3g24495 MSH7 (MUTS HOMOLOG 7) O.I. H.G.
L Os01g0578000 AK060971.1 - RecA bacterial DNA recombination protein familyprotein 2e-1 At2g45280 ATRAD51C O.I. H.G.
L Os01g0757800 AK067990.1 - UMUC-like DNA-repair protein family protein 8e-11 At5g44740 POLH (Y-FAMILT DNA POLYMERASE H) O.I. H.G.
L Os01g0777300 NM_191476.1 - DNA repair protein (XPGC)/yeast Rad family protein 1e-9 At1g29630 nuclease O.I. H.G.
L Os01g0799500 AU066087 - Methyladenine glycosylase family protein 1e-8 At3g12710 methyladenine glycosylase family protein O.I. H.G.
L Os01g0801000 AK101426.1 - Apurinic endonuclease-redox protein (DNA-(apurinicor apyrimidinic site) lyase) (EC 4.2.99.18) 3e-7 At2g41460 ARP O.I. H.G.
L Os01g0801100 AK102132.1 - Apurinic endonuclease-redox protein (DNA-(apurinicor apyrimidinic site) lyase) (EC 4.2.99.18) 3e+0 At5g50665 unknown protein O.I. H.G.
L Os01g0901200 AK103365.1 - RecA protein (Recombinase A) 7e-14 At2g19490 recA family protein O.I. H.G.
L Os01g0953500 AK058479.1 - C2 domain containing protein 1e-2 At5g55530 C2 domain-containing protein O.I. H.G.
L Os02g0125800 AK121932.1 - Transcription factor Tfb4 family protein 3e-15 At1g18340 basal transcription factor complex subunit-related O.I. H.G.
L Os02g0469300 AK063552.1 - ATP-binding region, ATPase-like domain containingprotein 2e-8 At4g24970 ATP-binding region, ATPase-like domain-containing protein O.I. H.G.
L Os02g0497500 AK106285.1 - Recombination/repair protein Rad50 family protein 4e-7 At2g31970 RAD50 O.I. H.G.
L Os02g0562100 - - - 0 - - O.I. H.G.
L Os02g0573200 AB024337.1 - Cryptochrome 1 6e-6 At4g08920 CRY1 (CRYPTOCHROME 1) O.I. H.G.
L Os03g0616300 AK102930.1 - DNA-directed polymerase kappa 2e-8 At1g49980 DNA-directed DNA polymerase/ damaged DNA binding O.I. H.G.
L Os03g0623000 - - - 0 - - O.I. H.G.
L Os04g0452100 AB073547.2 - Cryptochrome 1 apoprotein (Blue lightphotoreceptor) 5e-19 At4g08920 CRY1 (CRYPTOCHROME 1) O.I. H.G.
L Os04g0507000 AK067042.1 - DNA mismatch repair protein 9e-18 At3g24320 MSH1 (MUTL PROTEIN HOMOLOG 1) O.I. H.G.
L Os04g0548300 AK063594.1 - ARM repeat fold domain containing protein 7e-1 At3g25550 F-box family protein O.I. H.G.
L Os06g0151600 AB111516.1 - Peptidase S16, lon protease family protein 8e-8 At5g50340 ATP binding / damaged DNA binding / nucleoside-triphosphatase/ nucleotide binding O.I. H.G.
L Os06g0171800 AK120233.1 - Zn-finger Rad18 domain containing protein 3e-5 At1g48360 hydrolase, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleic acid binding / zinc ion binding O.I. H.G.
L Os06g0237200 AB099525.1 - DNA polymerase lambda 1e-15 At1g10520 DNA polymerase lambda (POLL) O.I. H.G.
L Os06g0643600 AK065376.1 - Formamidopyrimidine-DNA glycolase family protein 9e-4 At1g52500 ATMMH-1 (ARABIDOPSIS THALIANA MUTM HOMOLOG-1) O.I. H.G.
L Os07g0227600 - - - 0 - - O.I. H.G.
L Os07g0230500 9635.m01249 - Excinuclease ABC, C subunit, N-terminal domaincontaining protein 4e-8 At2g30350 endo/excinuclease amino terminal domain-containing protein O.I. H.G.
L Os07g0492100 AK067461.1 - UvrD/REP helicase family protein 4e-11 At4g25120 ATP binding / ATP-dependent DNA helicase/ DNA binding / hydrolase O.I. H.G.
L Os08g0304900 AK063295.1 - AtMMH-1 protein (F6D8.28 protein) 2e-2 At1g52500 ATMMH-1 (ARABIDOPSIS THALIANA MUTM HOMOLOG-1) O.I. H.G.
L Os08g0430700 AK101681.1 - Regulator of chromosomecondensation/beta-lactamase-inhibitor protein II domaincontaining protein 1e-5 At3g02510 regulator of chromosome condensation (RCC1) family protein O.I. H.G.
L Os08g0489300 AK104597.1 - DNA-3-methyladenine glycosidase I-like protein 8e-1 At3g25650 ASK15 (ARABIDOPSIS SKP1-LIKE 15) O.I. H.G.
L Os09g0401600 - - - 0 - - O.I. H.G.
L Os09g0420300 AK120582.1 - Methyladenine glycosylase family protein 1e-5 At1g80850 methyladenine glycosylase family protein O.I. H.G.
L Os09g0536000 AK103074.1 - AP endonuclease, family 1 protein 1e-3 At4g36050 endonuclease/exonuclease/phosphatase family protein O.I. H.G.
L Os10g0167600 AK111418.1 - CPD photolyase 3e-31 At1g12370 PHR1 (PHOTOLYASE 1) O.I. H.G.

ECC	Gene ID	Repr. ID	Gene name	Functional description	Ev	AGI code	Arabidopsis gene name	O.I.	H.G.
S	Os11g0146800	AB079874.1	-	RecA bacterial DNA recombination protein familyprotein	3e-49	At3g22880	DMC1 (DISRUPTION OF MEIOTIC CONTROL 1)	O.I.	H.G.
S	Os12g0143800	AB079873.1	-	Meiotic recombination protein DMC1 homolog	7e-38	At3g22880	DMC1 (DISRUPTION OF MEIOTIC CONTROL 1)	O.I.	H.G.
C	Os10g0518900	AK070764.1	-	DNA repair protein rad10 family protein	2e-1	At4g01050	hydroxyproline-rich glycoprotein family protein	O.I.	H.G.
C	Os11g0615800	AB080262.1	-	RAD51 homolog RAD51A	1e-73	At5g20850	ATRAD51	O.I.	H.G.
C	Os12g0497300	AB080264.1	-	RAD51 homolog RAD51B	7e-75	At5g20850	ATRAD51	O.I.	H.G.
L	Os01g0180600	NM_189554.1	-	MutS homolog 7 (Fragment)	1e-10	At3g24495	MSH7 (MUTS HOMOLOG 7)	O.I.	H.G.
L	Os01g0578000	AK060971.1	-	RecA bacterial DNA recombination protein familyprotein	2e-1	At2g45280	ATRAD51C	O.I.	H.G.
L	Os01g0757800	AK067990.1	-	UMUC-like DNA-repair protein family protein	8e-11	At5g44740	POLH (Y-FAMILT DNA POLYMERASE H)	O.I.	H.G.
L	Os01g0777300	NM_191476.1	-	DNA repair protein (XPGC)/yeast Rad family protein	1e-9	At1g29630	nuclease	O.I.	H.G.
L	Os01g0799500	AU066087	-	Methyladenine glycosylase family protein	1e-8	At3g12710	methyladenine glycosylase family protein	O.I.	H.G.
L	Os01g0801000	AK101426.1	-	Apurinic endonuclease-redox protein (DNA-(apurinicor apyrimidinic site) lyase) (EC 4.2.99.18)	3e-7	At2g41460	ARP	O.I.	H.G.
L	Os01g0801100	AK102132.1	-	Apurinic endonuclease-redox protein (DNA-(apurinicor apyrimidinic site) lyase) (EC 4.2.99.18)	3e+0	At5g50665	unknown protein	O.I.	H.G.
L	Os01g0901200	AK103365.1	-	RecA protein (Recombinase A)	7e-14	At2g19490	recA family protein	O.I.	H.G.
L	Os01g0953500	AK058479.1	-	C2 domain containing protein	1e-2	At5g55530	C2 domain-containing protein	O.I.	H.G.
L	Os02g0125800	AK121932.1	-	Transcription factor Tfb4 family protein	3e-15	At1g18340	basal transcription factor complex subunit-related	O.I.	H.G.
L	Os02g0469300	AK063552.1	-	ATP-binding region, ATPase-like domain containingprotein	2e-8	At4g24970	ATP-binding region, ATPase-like domain-containing protein	O.I.	H.G.
L	Os02g0497500	AK106285.1	-	Recombination/repair protein Rad50 family protein	4e-7	At2g31970	RAD50	O.I.	H.G.
L	Os02g0562100	-	-	-	0	-	-	O.I.	H.G.
L	Os02g0573200	AB024337.1	-	Cryptochrome 1	6e-6	At4g08920	CRY1 (CRYPTOCHROME 1)	O.I.	H.G.
L	Os03g0616300	AK102930.1	-	DNA-directed polymerase kappa	2e-8	At1g49980	DNA-directed DNA polymerase/ damaged DNA binding	O.I.	H.G.
L	Os03g0623000	-	-	-	0	-	-	O.I.	H.G.
L	Os04g0452100	AB073547.2	-	Cryptochrome 1 apoprotein (Blue lightphotoreceptor)	5e-19	At4g08920	CRY1 (CRYPTOCHROME 1)	O.I.	H.G.
L	Os04g0507000	AK067042.1	-	DNA mismatch repair protein	9e-18	At3g24320	MSH1 (MUTL PROTEIN HOMOLOG 1)	O.I.	H.G.
L	Os04g0548300	AK063594.1	-	ARM repeat fold domain containing protein	7e-1	At3g25550	F-box family protein	O.I.	H.G.
L	Os06g0151600	AB111516.1	-	Peptidase S16, lon protease family protein	8e-8	At5g50340	ATP binding / damaged DNA binding / nucleoside-triphosphatase/ nucleotide binding	O.I.	H.G.
L	Os06g0171800	AK120233.1	-	Zn-finger Rad18 domain containing protein	3e-5	At1g48360	hydrolase, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleic acid binding / zinc ion binding	O.I.	H.G.
L	Os06g0237200	AB099525.1	-	DNA polymerase lambda	1e-15	At1g10520	DNA polymerase lambda (POLL)	O.I.	H.G.
L	Os06g0643600	AK065376.1	-	Formamidopyrimidine-DNA glycolase family protein	9e-4	At1g52500	ATMMH-1 (ARABIDOPSIS THALIANA MUTM HOMOLOG-1)	O.I.	H.G.
L	Os07g0227600	-	-	-	0	-	-	O.I.	H.G.
L	Os07g0230500	9635.m01249	-	Excinuclease ABC, C subunit, N-terminal domaincontaining protein	4e-8	At2g30350	endo/excinuclease amino terminal domain-containing protein	O.I.	H.G.
L	Os07g0492100	AK067461.1	-	UvrD/REP helicase family protein	4e-11	At4g25120	ATP binding / ATP-dependent DNA helicase/ DNA binding / hydrolase	O.I.	H.G.
L	Os08g0304900	AK063295.1	-	AtMMH-1 protein (F6D8.28 protein)	2e-2	At1g52500	ATMMH-1 (ARABIDOPSIS THALIANA MUTM HOMOLOG-1)	O.I.	H.G.
L	Os08g0430700	AK101681.1	-	Regulator of chromosomecondensation/beta-lactamase-inhibitor protein II domaincontaining protein	1e-5	At3g02510	regulator of chromosome condensation (RCC1) family protein	O.I.	H.G.
L	Os08g0489300	AK104597.1	-	DNA-3-methyladenine glycosidase I-like protein	8e-1	At3g25650	ASK15 (ARABIDOPSIS SKP1-LIKE 15)	O.I.	H.G.
L	Os09g0401600	-	-	-	0	-	-	O.I.	H.G.
L	Os09g0420300	AK120582.1	-	Methyladenine glycosylase family protein	1e-5	At1g80850	methyladenine glycosylase family protein	O.I.	H.G.
L	Os09g0536000	AK103074.1	-	AP endonuclease, family 1 protein	1e-3	At4g36050	endonuclease/exonuclease/phosphatase family protein	O.I.	H.G.
L	Os10g0167600	AK111418.1	-	CPD photolyase	3e-31	At1g12370	PHR1 (PHOTOLYASE 1)	O.I.	H.G.

The upper GO terms

Process ID Gene number Process name
GO:0006259 16 The chemical reactions and pathways involving DNA, deoxyribonucleic acid, 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.
GO:0034984 0 A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

Process ID	Gene number	Process name
GO:0006259	16	The chemical reactions and pathways involving DNA, deoxyribonucleic acid, 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.
GO:0034984	0	A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

The lower GO terms

Process ID Gene number Process name
GO:0000012 0 The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.
GO:0000725 0 A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
GO:0000726 0 A DNA repair process in which that does not require the exchange of genetic material between the broken DNA molecule and a homologous region of DNA.
GO:0000731 0 Synthesis of DNA that proceeds from the broken 3' single-strand DNA end uses the homologous intact duplex as the template.
GO:0006284 3 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.
GO:0006289 11 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).
GO:0006290 0 The repair of UV-induced T-T, C-T and C-C dimers.
GO:0006298 11 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.
GO:0006301 0 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.
GO:0006302 2 The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
GO:0006307 0 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).
GO:0010213 0 A DNA repair process that is involved in repairing UV-induced DNA damage under non-photoreactivating conditions. The mechanism by which this repair process operates has not yet been completely elucidated.
GO:0043504 0 The process of restoring mitochondrial DNA after damage.
GO:0045004 0 Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.
GO:0045020 0 DNA repair pathways that tend to increase the endogenous mutation rate.
GO:0045021 0 DNA repair pathways that do not increase the mutation rate above spontaneous background levels, e.g. excision and recombination pathways.
GO:0046787 0 The process of restoring viral DNA after damage or errors in replication.
GO:0051103 0 The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, as occurs during DNA repair.
GO:0070914 0 A DNA repair process that is initiated by an endonuclease that introduces a single-strand incision immediately 5' of a UV-induced damage site. UV-damage excision repair acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs).

Process ID	Gene number	Process name
GO:0000012	0	The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.
GO:0000725	0	A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
GO:0000726	0	A DNA repair process in which that does not require the exchange of genetic material between the broken DNA molecule and a homologous region of DNA.
GO:0000731	0	Synthesis of DNA that proceeds from the broken 3' single-strand DNA end uses the homologous intact duplex as the template.
GO:0006284	3	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.
GO:0006289	11	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).
GO:0006290	0	The repair of UV-induced T-T, C-T and C-C dimers.
GO:0006298	11	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.
GO:0006301	0	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.
GO:0006302	2	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
GO:0006307	0	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).
GO:0010213	0	A DNA repair process that is involved in repairing UV-induced DNA damage under non-photoreactivating conditions. The mechanism by which this repair process operates has not yet been completely elucidated.
GO:0043504	0	The process of restoring mitochondrial DNA after damage.
GO:0045004	0	Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.
GO:0045020	0	DNA repair pathways that tend to increase the endogenous mutation rate.
GO:0045021	0	DNA repair pathways that do not increase the mutation rate above spontaneous background levels, e.g. excision and recombination pathways.
GO:0046787	0	The process of restoring viral DNA after damage or errors in replication.
GO:0051103	0	The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, as occurs during DNA repair.
GO:0070914	0	A DNA repair process that is initiated by an endonuclease that introduces a single-strand incision immediately 5' of a UV-induced damage site. UV-damage excision repair acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs).

Comparison with co-expressed genes

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Query process ID	GO:0006281
Process name	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.
Organism	Oryza sativa