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PATHWAY ONTOLOGY - ANNOTATIONS

The Pathway Ontology (PW), is currently being developed at the Rat Genome Database. For more information about this vocabulary, please see Petri et al. The rat genome database pathway portal. Database (Oxford). 2011 Apr 8;2011:bar010. Print 2011 or contact us (http://rgd.mcw.edu/contact/index.shtml).
Term:DNA modification pathway
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Accession:PW:0001340 term browser browse the term
Definition:DNA modification is a component of the chromatin modification pathway. At least four DNA modification types are known. The modifications are recognized by specific readers and removed by eraser enzymes.
Synonyms:related_synonym: DNA modification
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show annotations for term's descendants           Sort by:
DNA modification pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cxxc1 CXXC finger protein 1 ISO RGD PMID:23697932 RGD:9479164 NCBI chr18:67,813,185...67,818,556
Ensembl chr18:67,813,206...67,818,551 		JBrowse link
G Dnmt1 DNA methyltransferase 1 ISO RGD PMID:22770212 PMID:24825349 RGD:8695943, RGD:8695944 NCBI chr 8:19,440,611...19,486,659
Ensembl chr 8:19,440,611...19,486,659 		JBrowse link
G Dnmt3a DNA methyltransferase 3 alpha ISO RGD PMID:22770212 PMID:24825349 RGD:8695943, RGD:8695944 NCBI chr 6:26,791,517...26,902,161
Ensembl chr 6:26,822,609...26,896,687 		JBrowse link
G Dnmt3b DNA methyltransferase 3 beta ISO RGD PMID:22770212 PMID:24825349 RGD:8695943, RGD:8695944 NCBI chr 3:142,130,588...142,169,128
Ensembl chr 3:142,130,592...142,169,124 		JBrowse link
G Ebf1 EBF transcription factor 1 ISO RGD PMID:24825349 RGD:8695944 NCBI chr10:29,095,858...29,489,142
Ensembl chr10:29,099,933...29,487,665 		JBrowse link
G Kdm2a lysine demethylase 2A ISO RGD PMID:23697932 RGD:9479164 NCBI chr 1:201,612,427...201,682,359
Ensembl chr 1:201,612,453...201,680,787 		JBrowse link
G Kdm2b lysine demethylase 2B ISO RGD PMID:23697932 RGD:9479164 NCBI chr12:33,566,530...33,701,366
Ensembl chr12:33,574,657...33,701,355 		JBrowse link
G Kmt2a lysine methyltransferase 2A ISO RGD PMID:23697932 RGD:9479164 NCBI chr 8:45,116,763...45,193,320
Ensembl chr 8:45,118,814...45,193,181 		JBrowse link
G Kmt2c lysine methyltransferase 2C ISO RGD PMID:23697932 RGD:9479164 NCBI chr 4:9,620,638...9,834,787
Ensembl chr 4:9,609,627...9,833,539 		JBrowse link
G Mbd1 methyl-CpG binding domain protein 1 ISO RGD PMID:23324617 RGD:8695954 NCBI chr18:67,869,870...67,884,501
Ensembl chr18:67,869,992...67,886,554 		JBrowse link
G Mbd2 methyl-CpG binding domain protein 2 ISO RGD PMID:23324617 RGD:8695954 NCBI chr18:64,174,002...64,240,795
Ensembl chr18:64,174,002...64,240,794 		JBrowse link
G Mbd4 methyl-CpG binding domain 4 DNA glycosylase ISO RGD PMID:23324617 RGD:8695954 NCBI chr 4:148,893,049...148,904,833
Ensembl chr 4:148,894,280...148,904,982 		JBrowse link
G Mecp2 methyl CpG binding protein 2 ISO RGD PMID:23324617 RGD:8695954 NCBI chr  X:151,781,177...151,844,687
Ensembl chr  X:151,789,930...151,844,689 		JBrowse link
G Nanog Nanog homeobox ISO RGD PMID:24825349 RGD:8695944 NCBI chr 4:155,943,737...155,951,116
Ensembl chr 4:155,943,737...155,951,116 		JBrowse link
G Ogt O-linked N-acetylglucosamine (GlcNAc) transferase ISO RGD PMID:24825349 RGD:8695944 NCBI chr  X:66,771,278...66,816,148
Ensembl chr  X:66,771,349...66,816,146 		JBrowse link
G Pparg peroxisome proliferator-activated receptor gamma ISO RGD PMID:24825349 RGD:8695944 NCBI chr 4:148,423,102...148,548,471
Ensembl chr 4:148,423,194...148,548,468 		JBrowse link
G Prdm14 PR/SET domain 14 ISO RGD PMID:24825349 RGD:8695944 NCBI chr 5:6,082,163...6,092,712
Ensembl chr 5:6,082,442...6,092,712 		JBrowse link
G Sin3a SIN3 transcription regulator family member A ISO RGD PMID:24825349 RGD:8695944 NCBI chr 8:57,481,539...57,536,195
Ensembl chr 8:57,481,573...57,536,192 		JBrowse link
G Spi1 Spi-1 proto-oncogene ISO RGD PMID:24825349 RGD:8695944 NCBI chr 3:77,059,744...77,093,730
Ensembl chr 3:77,073,012...77,092,393 		JBrowse link
G Tet1 tet methylcytosine dioxygenase 1 ISO RGD PMID:22770212 PMID:24825349 RGD:8695943, RGD:8695944 NCBI chr20:25,761,042...25,840,926
Ensembl chr20:25,768,120...25,833,052 		JBrowse link
G Tet2 tet methylcytosine dioxygenase 2 ISO RGD PMID:22770212 PMID:24825349 RGD:8695943, RGD:8695944 NCBI chr 2:221,988,645...222,072,813
Ensembl chr 2:221,988,645...222,072,534 		JBrowse link
G Tet3 tet methylcytosine dioxygenase 3 ISO RGD PMID:22770212 PMID:23697932 PMID:24825349 RGD:8695943, RGD:9479164, RGD:8695944 NCBI chr 4:115,867,412...115,964,433
Ensembl chr 4:115,871,265...115,964,193 		JBrowse link
G Uhrf1 ubiquitin-like with PHD and ring finger domains 1 ISO RGD PMID:23324617 RGD:8695954 NCBI chr 9:1,133,117...1,154,639
Ensembl chr 9:1,134,909...1,154,631 		JBrowse link
G Uhrf2 ubiquitin like with PHD and ring finger domains 2 ISO RGD PMID:23324617 RGD:8695954 NCBI chr 1:227,814,639...227,877,907
Ensembl chr 1:227,814,963...227,877,904 		JBrowse link
G Zbtb33 zinc finger and BTB domain containing 33 ISO RGD PMID:23324617 RGD:8695954 NCBI chr  X:116,963,337...116,970,547
Ensembl chr  X:116,963,347...116,971,023 		JBrowse link
G Zbtb38 zinc finger and BTB domain containing 38 ISO RGD PMID:23324617 RGD:8695954 NCBI chr 8:97,284,617...97,288,518
Ensembl chr 8:97,280,993...97,485,625 		JBrowse link
G Zbtb4 zinc finger and BTB domain containing 4 ISO RGD PMID:23324617 RGD:8695954 NCBI chr10:54,480,698...54,501,492
Ensembl chr10:54,485,071...54,501,492 		JBrowse link
G Zfp57 zinc finger protein 57 ISO RGD PMID:23324617 RGD:8695954 NCBI chr20:1,521,323...1,534,884
Ensembl chr20:1,521,323...1,529,846 		JBrowse link
altered DNA modification pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mbd4 methyl-CpG binding domain 4 DNA glycosylase ISO in silico assessment of loss of DNA-protein interactions and observed enhancement of DNA repair capacity (DRC) in the context of nucleotide excision repair (NER) pathway for SNP RGD PMID:24004570 RGD:9588971 NCBI chr 4:148,893,049...148,904,833
Ensembl chr 4:148,894,280...148,904,982 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  pathway 6092
    regulatory pathway 3867
      pathway pertinent to DNA replication and repair, cell cycle, maintenance of genomic integrity, RNA and protein biosynthesis 1738
        chromatin modification/remodeling pathway 268
          chromatin modification pathway 206
            DNA modification pathway 28
              altered DNA modification pathway 1
Path 2
Term Annotations click to browse term
  pathway 6092
    regulatory pathway 3867
      pathway pertinent to DNA replication and repair, cell cycle, maintenance of genomic integrity, RNA and protein biosynthesis 1738
        DNA damage response pathway 405
          DNA repair pathway 384
            chromatin modification/remodeling pathway 268
              chromatin modification pathway 206
                DNA modification pathway 28
                  altered DNA modification pathway 1
paths to the root