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ONTOLOGY REPORT - ANNOTATIONS


Term:DNA methylation or demethylation
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Accession:GO:0044728 term browser browse the term
Definition:The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule.
Synonyms:related_synonym: changes in DNA methylation


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C-5 methylation of cytosine term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:1600115
G Dnmt3a DNA methyltransferase 3 alpha JBrowse link 6 28,205,375 28,346,052 RGD:1600115
G Dnmt3b DNA methyltransferase 3 beta JBrowse link 3 149,131,541 149,170,061 RGD:1624291
G Stpg4 sperm-tail PG-rich repeat containing 4 JBrowse link 6 11,014,596 11,063,509 RGD:1624291
DNA demethylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Aicda activation-induced cytidine deaminase JBrowse link 4 155,359,909 155,371,104 RGD:1624291
RGD:13792537
G Alkbh1 alkB homolog 1, histone H2A dioxygenase JBrowse link 6 111,456,096 111,476,829 RGD:1624291
G Alkbh4 alkB homolog 4, lysine demethylase JBrowse link 12 23,568,204 23,574,133 RGD:1624291
G Apex1 apurinic/apyrimidinic endodeoxyribonuclease 1 JBrowse link 15 27,849,943 27,852,083 RGD:1624291
RGD:1600115
G Apobec1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 JBrowse link 4 155,386,367 155,414,034 RGD:1624291
RGD:13792537
RGD:1600115
G Apobec2 apolipoprotein B mRNA editing enzyme catalytic subunit 2 JBrowse link 9 14,529,218 14,542,731 RGD:1624291
RGD:13792537
G Apobec3 apolipoprotein B mRNA editing enzyme catalytic subunit 3 JBrowse link 7 121,108,108 121,128,346 RGD:13792537
G Fto FTO, alpha-ketoglutarate dependent dioxygenase JBrowse link 19 16,774,549 17,115,098 RGD:1624291
G Tdg thymine-DNA glycosylase JBrowse link 7 27,194,000 27,213,676 RGD:1624291
G Tet1 tet methylcytosine dioxygenase 1 JBrowse link 20 27,359,122 27,438,039 RGD:1624291
RGD:13792537
G Tet2 tet methylcytosine dioxygenase 2 JBrowse link 2 238,719,389 238,802,975 RGD:1624291
RGD:13792537
G Tet3 tet methylcytosine dioxygenase 3 JBrowse link 4 115,060,702 115,160,800 RGD:1624291
RGD:13792537
DNA demethylation of male pronucleus term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Stpg4 sperm-tail PG-rich repeat containing 4 JBrowse link 6 11,014,596 11,063,509 RGD:1624291
G Tet3 tet methylcytosine dioxygenase 3 JBrowse link 4 115,060,702 115,160,800 RGD:1624291
DNA hypermethylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:9588311
G Morc1 MORC family CW-type zinc finger 1 JBrowse link 11 54,762,654 55,044,581 RGD:1624291
DNA methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Atf7ip activating transcription factor 7 interacting protein JBrowse link 4 170,476,998 170,563,063 RGD:1624291
G Baz2a bromodomain adjacent to zinc finger domain, 2A JBrowse link 7 2,518,267 2,548,840 RGD:1624291
G Bend3 BEN domain containing 3 JBrowse link 20 48,248,193 48,270,905 RGD:1624291
G Bmi1 BMI1 proto-oncogene, polycomb ring finger JBrowse link 17 85,360,439 85,370,283 RGD:1624291
G Ctcf CCCTC-binding factor JBrowse link 19 37,600,151 37,649,674 RGD:1600115
RGD:1624291
G Cyp1a1 cytochrome P450, family 1, subfamily a, polypeptide 1 JBrowse link 8 62,472,087 62,478,122 RGD:25823175
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:1624291
G Dnmt3a DNA methyltransferase 3 alpha JBrowse link 6 28,205,375 28,346,052 RGD:8554662
RGD:1624291
G Dnmt3b DNA methyltransferase 3 beta JBrowse link 3 149,131,541 149,170,061 RGD:1624291
G Dnmt3l DNA methyltransferase 3 like JBrowse link 20 11,344,513 11,359,090 RGD:1624291
G Ehmt1 euchromatic histone lysine methyltransferase 1 JBrowse link 3 1,966,974 2,123,858 RGD:1624291
G Ehmt2 euchromatic histone lysine methyltransferase 2 JBrowse link 20 4,576,033 4,592,980 RGD:1624291
G Ezh2 enhancer of zeste 2 polycomb repressive complex 2 subunit JBrowse link 4 77,284,404 77,347,011 RGD:1624291
G Gnas GNAS complex locus JBrowse link 3 172,374,957 172,434,988 RGD:1624291
G Hells helicase, lymphoid specific JBrowse link 1 257,901,856 257,953,889 RGD:1624291
RGD:13792537
G Kmt2a lysine methyltransferase 2A JBrowse link 8 49,110,407 49,185,872 RGD:1624291
G Kmt2e lysine methyltransferase 2E JBrowse link 4 8,187,751 8,255,578 RGD:1624291
G LOC100911660 lymphocyte-specific helicase-like JBrowse link 1 257,614,688 257,660,184 RGD:13792537
G Mta2 metastasis associated 1 family, member 2 JBrowse link 1 225,140,863 225,149,584 RGD:1624291
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase JBrowse link 17 66,210,444 66,295,014 RGD:10054082
G Mtrr 5-methyltetrahydrofolate-homocysteine methyltransferase reductase JBrowse link 1 37,743,089 37,774,485 RGD:1624291
RGD:1600115
G Ppm1d protein phosphatase, Mg2+/Mn2+ dependent, 1D JBrowse link 10 72,909,550 72,945,884 RGD:1624291
DNA methylation involved in embryo development term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:1600115
RGD:1624291
G Dnmt3a DNA methyltransferase 3 alpha JBrowse link 6 28,205,375 28,346,052 RGD:1624291
G Dnmt3b DNA methyltransferase 3 beta JBrowse link 3 149,131,541 149,170,061 RGD:1624291
G Trim28 tripartite motif-containing 28 JBrowse link 1 65,544,369 65,551,043 RGD:1624291
G Zfp57 zinc finger protein 57 JBrowse link 20 2,014,177 2,020,488 RGD:1624291
RGD:1600115
DNA methylation involved in gamete generation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Asz1 ankyrin repeat, SAM and basic leucine zipper domain containing 1 JBrowse link 4 45,358,574 45,414,177 RGD:1624291
G Ctcfl CCCTC-binding factor like JBrowse link 3 171,145,203 171,168,375 RGD:1624291
G Ddx4 DEAD-box helicase 4 JBrowse link 2 44,447,610 44,504,263 RGD:1624291
RGD:1600115
G Dnmt3a DNA methyltransferase 3 alpha JBrowse link 6 28,205,375 28,346,052 RGD:1624291
G Dnmt3l DNA methyltransferase 3 like JBrowse link 20 11,344,513 11,359,090 RGD:1624291
RGD:1600115
G Fkbp6 FKBP prolyl isomerase 6 JBrowse link 12 24,365,941 24,438,088 RGD:1624291
RGD:1600115
G Kdm1b lysine demethylase 1B JBrowse link 17 17,987,972 18,028,808 RGD:1624291
G Mael maelstrom spermatogenic transposon silencer JBrowse link 13 84,412,569 84,452,140 RGD:1624291
G Morc1 MORC family CW-type zinc finger 1 JBrowse link 11 54,762,654 55,044,581 RGD:1624291
G Mov10l1 Mov10 like RISC complex RNA helicase 1 JBrowse link 7 129,973,391 130,039,306 RGD:1624291
G Piwil2 piwi-like RNA-mediated gene silencing 2 JBrowse link 15 52,037,693 52,116,277 RGD:1624291
G Piwil4 piwi-like RNA-mediated gene silencing 4 JBrowse link 8 13,208,774 13,251,970 RGD:1600115
RGD:1624291
G Pld6 phospholipase D family, member 6 JBrowse link 10 46,142,313 46,145,774 RGD:1624291
G Prmt7 protein arginine methyltransferase 7 JBrowse link 19 38,189,605 38,237,155 RGD:1624291
RGD:1600115
G Tdrd1 tudor domain containing 1 JBrowse link 1 277,639,670 277,685,236 RGD:1624291
G Tdrd12 tudor domain containing 12 JBrowse link 1 91,739,126 91,811,577 RGD:1624291
G Tdrd5 tudor domain containing 5 JBrowse link 13 73,872,637 73,922,640 RGD:1600115
RGD:1624291
G Tdrd9 tudor domain containing 9 JBrowse link 6 136,536,636 136,650,481 RGD:1624291
RGD:1600115
G Tdrkh tudor and KH domain containing JBrowse link 2 195,649,813 195,674,217 RGD:1624291
DNA methylation on adenine term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Mettl4 methyltransferase like 4 JBrowse link 9 119,871,519 119,953,248 RGD:1624291
G N6amt1 N-6 adenine-specific DNA methyltransferase 1 JBrowse link 11 27,004,335 27,016,690 RGD:1624291
DNA methylation on cytosine term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:9588218
RGD:1624291
G Dnmt3a DNA methyltransferase 3 alpha JBrowse link 6 28,205,375 28,346,052 RGD:9588218
G Dnmt3l DNA methyltransferase 3 like JBrowse link 20 11,344,513 11,359,090 RGD:1624291
RGD:1600115
DNA methylation on cytosine within a CG sequence term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:2301219
G Ehmt2 euchromatic histone lysine methyltransferase 2 JBrowse link 20 4,576,033 4,592,980 RGD:1624291
G Smarca4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 JBrowse link 8 22,648,323 22,739,468 RGD:1624291
hypermethylation of CpG island term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt3a DNA methyltransferase 3 alpha JBrowse link 6 28,205,375 28,346,052 RGD:1624291
G Gsk3a glycogen synthase kinase 3 alpha JBrowse link 1 82,097,244 82,108,238 RGD:1624291
G Gsk3b glycogen synthase kinase 3 beta JBrowse link 11 65,060,884 65,208,842 RGD:1624291
G Spi1 Spi-1 proto-oncogene JBrowse link 3 79,918,127 79,937,708 RGD:1624291
hypomethylation of CpG island term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Pik3ca phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha JBrowse link 2 118,831,350 118,861,456 RGD:1624291
G Zmpste24 zinc metallopeptidase STE24 JBrowse link 5 139,982,404 140,015,541 RGD:1624291
negative regulation of DNA demethylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07015759.1 RGD:13792537
G AABR07017902.2 RGD:13792537
G AABR07026842.1 RGD:13792537
G AABR07058017.1 RGD:13792537
G AABR07061871.1 RGD:13792537
G Dppa3 developmental pluripotency-associated 3 JBrowse link 4 155,437,675 155,441,059 RGD:1600115
RGD:13792537
RGD:1624291
G Dppa3l1 developmental pluripotency associated 3-like 1 JBrowse link 8 60,683,180 60,683,658 RGD:13792537
G Gata3 GATA binding protein 3 JBrowse link 17 72,419,752 72,452,043 RGD:1624291
G LOC679766 similar to developmental pluripotency-associated 3 JBrowse link 14 74,094,652 74,095,296 RGD:13792537
G Trim28 tripartite motif-containing 28 JBrowse link 1 65,544,369 65,551,043 RGD:1624291
negative regulation of DNA methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt3l DNA methyltransferase 3 like JBrowse link 20 11,344,513 11,359,090 RGD:1624291
RGD:1600115
G Kmt2a lysine methyltransferase 2A JBrowse link 8 49,110,407 49,185,872 RGD:1624291
oxidative DNA demethylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Alkbh1 alkB homolog 1, histone H2A dioxygenase JBrowse link 6 111,456,096 111,476,829 RGD:1600115
G Alkbh2 alkB homolog 2, alpha-ketoglutarate-dependent dioxygenase JBrowse link 12 48,257,575 48,262,244 RGD:1624291
RGD:13792537
G Alkbh4 alkB homolog 4, lysine demethylase JBrowse link 12 23,568,204 23,574,133 RGD:1600115
oxidative single-stranded DNA demethylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Alkbh3 alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase JBrowse link 3 82,874,242 82,907,467 RGD:1600115
RGD:1624291
G Fto FTO, alpha-ketoglutarate dependent dioxygenase JBrowse link 19 16,774,549 17,115,098 RGD:1624291
RGD:13792537
RGD:1600115
positive regulation of DNA demethylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Otud4 OTU deubiquitinase 4 JBrowse link 19 31,895,753 31,942,509 RGD:1624291
G Stpg4 sperm-tail PG-rich repeat containing 4 JBrowse link 6 11,014,596 11,063,509 RGD:1624291
G Tox thymocyte selection-associated high mobility group box JBrowse link 5 19,892,698 20,189,721 RGD:1624291
G Usp7 ubiquitin specific peptidase 7 JBrowse link 10 6,930,462 7,019,910 RGD:1600115
RGD:1624291
G Usp9x ubiquitin specific peptidase 9, X-linked JBrowse link X 10,510,033 10,660,555 RGD:1624291
positive regulation of DNA methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt3l DNA methyltransferase 3 like JBrowse link 20 11,344,513 11,359,090 RGD:1624291
RGD:1600115
G Mecp2 methyl CpG binding protein 2 JBrowse link X 156,650,389 156,713,813 RGD:1624291
RGD:1600115
G Myc MYC proto-oncogene, bHLH transcription factor JBrowse link 7 102,586,313 102,591,240 RGD:1624291
G Wt1 WT1 transcription factor JBrowse link 3 95,133,221 95,180,574 RGD:1624291
RGD:1600115
protection of DNA demethylation of female pronucleus term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07015759.1 RGD:13792537
G AABR07017902.2 RGD:13792537
G AABR07026842.1 RGD:13792537
G AABR07058017.1 RGD:13792537
G AABR07061871.1 RGD:13792537
G Dppa3 developmental pluripotency-associated 3 JBrowse link 4 155,437,675 155,441,059 RGD:1600115
RGD:13792537
RGD:1624291
G Dppa3l1 developmental pluripotency associated 3-like 1 JBrowse link 8 60,683,180 60,683,658 RGD:13792537
G LOC679766 similar to developmental pluripotency-associated 3 JBrowse link 14 74,094,652 74,095,296 RGD:13792537
regulation of DNA methylation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Brca1 BRCA1, DNA repair associated JBrowse link 10 89,394,821 89,455,093 RGD:1624291
RGD:1600115
G Ehmt2 euchromatic histone lysine methyltransferase 2 JBrowse link 20 4,576,033 4,592,980 RGD:9588218
G Ftx FTX transcript, XIST regulator JBrowse link X 74,440,265 74,484,164 RGD:1624291
G Grhl2 grainyhead-like transcription factor 2 JBrowse link 7 76,058,623 76,197,360 RGD:1624291
G H1f8 H1.8 linker histone JBrowse link 4 147,844,658 147,849,779 RGD:1624291
RGD:1600115
G Kdm1b lysine demethylase 1B JBrowse link 17 17,987,972 18,028,808 RGD:1624291
G Mbd1 methyl-CpG binding domain protein 1 JBrowse link 18 70,248,568 70,263,190 RGD:9588647
G Mbd2 methyl-CpG binding domain protein 2 JBrowse link 18 65,814,026 65,885,115 RGD:9588647
G Mbd3 methyl-CpG binding domain protein 3 JBrowse link 7 12,179,046 12,186,251 RGD:9588647
G Mecp2 methyl CpG binding protein 2 JBrowse link X 156,650,389 156,713,813 RGD:9588647
G Mis18a MIS18 kinetochore protein A JBrowse link 11 30,880,231 30,893,262 RGD:1624291
G Mphosph8 M-phase phosphoprotein 8 JBrowse link 15 36,918,843 36,946,712 RGD:1624291
RGD:1600115
G Parp1 poly (ADP-ribose) polymerase 1 JBrowse link 13 98,857,255 98,889,444 RGD:10413908
G Prdm14 PR/SET domain 14 JBrowse link 5 5,710,076 5,730,560 RGD:1624291
G Prmt5 protein arginine methyltransferase 5 JBrowse link 15 33,156,508 33,165,893 RGD:9491827
G Rlf RLF zinc finger JBrowse link 5 140,107,144 140,162,698 RGD:1624291
G Tet1 tet methylcytosine dioxygenase 1 JBrowse link 20 27,359,122 27,438,039 RGD:1624291
G Zmpste24 zinc metallopeptidase STE24 JBrowse link 5 139,982,404 140,015,541 RGD:1624291

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 19858
    metabolic process 12096
      organic substance metabolic process 11494
        macromolecule metabolic process 9943
          macromolecule modification 4106
            DNA modification 105
              DNA methylation or demethylation 93
                DNA demethylation + 29
                DNA methylation + 76
                changes to DNA methylation involved in embryo development + 15
Path 2
Term Annotations click to browse term
  biological_process 19858
    metabolic process 12096
      cellular metabolic process 10917
        cellular nitrogen compound metabolic process 6542
          nucleobase-containing compound metabolic process 5344
            nucleic acid metabolic process 4850
              DNA metabolic process 911
                DNA modification 105
                  DNA methylation or demethylation 93
                    DNA demethylation + 29
                    DNA methylation + 76
                    changes to DNA methylation involved in embryo development + 15
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.