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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 (https://rgd.mcw.edu/rgdweb/contact/contactus.html).
Term:altered pathway pertinent to DNA replication and repair, cell cycle, maintenance of genomic integrity, RNA and protein biosynthesis
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Accession:PW:0000290 term browser browse the term
Definition:Those pathways involved in and/or controlling DNA replication, cell cycle, DNA repair and preservation of genomic integrity, RNA and protein biosynthesis that deviate from what their normal course should be. Such aberrant pathways, alone or in combination with other pathways underlie various diseases.


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altered androgen signaling pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ar androgen receptor ISO RGD PMID:18008377 PMID:23759327 RGD:2326139, RGD:8693397 NCBI chr  X:67,135,317...67,304,476
Ensembl chr  X:63,104,771...63,273,925 		JBrowse link
G Ncoa2 nuclear receptor coactivator 2 ISO RGD PMID:23759327 RGD:8693397 NCBI chr 5:10,618,712...10,852,776
Ensembl chr 5:5,835,706...6,067,451 		JBrowse link
G Ncor2 nuclear receptor co-repressor 2 ISO RGD PMID:23759327 RGD:8693397 NCBI chr12:37,127,736...37,289,612
Ensembl chr12:31,466,412...31,628,319 		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
altered G1/S transition pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cdkn2a cyclin-dependent kinase inhibitor 2A ISO RGD PMID:18772397 RGD:5490966 NCBI chr 5:109,100,763...109,114,448
Ensembl chr 5:103,984,949...104,003,149 		JBrowse link
altered hypoxia inducible factor pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Vhl von Hippel-Lindau tumor suppressor ISO RGD PMID:22035299 RGD:6907133 NCBI chr 4:148,328,099...148,334,992
Ensembl chr 4:146,772,468...146,779,377 		JBrowse link
altered mismatch repair pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mlh1 mutL homolog 1 ISO RGD PMID:11900875 PMID:19078924 RGD:2306714, RGD:4143515 NCBI chr 8:120,074,871...120,112,109
Ensembl chr 8:111,196,468...111,233,617 		JBrowse link
G Msh2 mutS homolog 2 ISO RGD PMID:11900875 RGD:2306714 NCBI chr 6:12,567,368...12,626,534
Ensembl chr 6:6,813,795...6,872,938 		JBrowse link
G Msh6 mutS homolog 6 ISO RGD PMID:11900875 RGD:2306714 NCBI chr 6:12,316,190...12,333,505
Ensembl chr 6:6,562,632...6,579,956 		JBrowse link
G Pms1 PMS1 homolog 1, mismatch repair system component ISO RGD PMID:11900875 RGD:2306714 NCBI chr 9:55,721,393...55,832,225
Ensembl chr 9:48,253,410...48,340,237 		JBrowse link
G Pms2 PMS1 homolog 2, mismatch repair system component ISO RGD PMID:11900875 RGD:2306714 NCBI chr12:15,790,478...15,814,790
Ensembl chr12:10,676,764...10,701,066 		JBrowse link
altered nucleotide excision repair pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ddb1 damage-specific DNA binding protein 1 ISO RGD PMID:22824526 RGD:7246919 NCBI chr 1:207,252,890...207,278,685
Ensembl chr 1:207,252,890...207,278,676 		JBrowse link
G Ercc2 ERCC excision repair 2, TFIIH core complex helicase subunit ISO RGD PMID:22824526 RGD:7246919 NCBI chr 1:88,161,342...88,175,102
Ensembl chr 1:79,033,326...79,047,102 		JBrowse link
G Ercc3 ERCC excision repair 3, TFIIH core complex helicase subunit ISO RGD PMID:22824526 RGD:7246919 NCBI chr18:24,157,831...24,188,543
Ensembl chr18:23,883,580...23,914,329 		JBrowse link
G Ercc4 ERCC excision repair 4, endonuclease catalytic subunit ISO in silico assessment of alteration of DNA-protein, protein-protein interactions and observed reduction of DNA repair capacity in the context of nucleotide excision repair pathway for SNP RGD PMID:22824526 PMID:24004570 RGD:7246919, RGD:9588971 NCBI chr10:2,926,085...2,958,176
Ensembl chr10:2,419,038...2,448,369
Ensembl chr10:2,419,038...2,448,369 		JBrowse link
G Ercc5 ERCC excision repair 5, endonuclease ISO RGD PMID:22824526 RGD:7246919 NCBI chr 9:53,801,471...53,846,611
Ensembl chr 9:46,309,389...46,354,472 		JBrowse link
G Ercc6 ERCC excision repair 6, chromatin remodeling factor ISO RGD PMID:22824526 RGD:7246919 NCBI chr16:7,771,311...7,841,895
Ensembl chr16:7,765,013...7,835,587 		JBrowse link
G Ercc8 ERCC excision repair 8, CSA ubiquitin ligase complex subunit ISO RGD PMID:22824526 RGD:7246919 NCBI chr 2:41,380,901...41,418,294
Ensembl chr 2:39,647,452...39,684,859 		JBrowse link
G Xpa XPA, DNA damage recognition and repair factor ISO RGD PMID:22824526 RGD:7246919 NCBI chr 5:65,227,281...65,275,784
Ensembl chr 5:60,431,673...60,475,726 		JBrowse link
G Xpc XPC complex subunit, DNA damage recognition and repair factor ISO RGD PMID:22824526 RGD:7246919 NCBI chr 4:125,550,833...125,578,084
Ensembl chr 4:123,993,666...124,021,010 		JBrowse link
altered p53 signaling pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ets1 ETS proto-oncogene 1, transcription factor ISO RGD PMID:22713868 RGD:8663430 NCBI chr 8:31,045,909...31,168,010
Ensembl chr 8:31,045,945...31,168,010 		JBrowse link
G Mdm2 MDM2 proto-oncogene ISO RGD PMID:19165225 PMID:23262034 RGD:2316186, RGD:8663434 NCBI chr 7:53,290,660...53,315,205
Ensembl chr 7:53,290,664...53,314,915 		JBrowse link
G Mdm4 MDM4 regulator of p53 ISO RGD PMID:23262034 RGD:8663434 NCBI chr13:44,432,596...44,516,165
Ensembl chr13:44,406,213...44,474,226 		JBrowse link
G Mre11 MRE11 homolog, double strand break repair nuclease ISO RGD PMID:23263379 RGD:8663431 NCBI chr 8:19,900,211...19,961,906
Ensembl chr 8:11,632,354...11,678,279 		JBrowse link
G Nfya nuclear transcription factor Y subunit alpha ISO RGD PMID:23263379 PMID:22713868 RGD:8663431, RGD:8663430 NCBI chr 9:12,587,437...12,613,911
Ensembl chr 9:12,586,259...12,613,898 		JBrowse link
G Nfyb nuclear transcription factor Y subunit beta ISO RGD PMID:23263379 PMID:22713868 RGD:8663431, RGD:8663430 NCBI chr 7:20,964,988...20,980,569
Ensembl chr 7:20,964,993...20,980,565 		JBrowse link
G Nfyc nuclear transcription factor Y subunit gamma ISO RGD PMID:23263379 PMID:22713868 RGD:8663431, RGD:8663430 NCBI chr 5:134,336,802...134,405,372
Ensembl chr 5:134,336,808...134,405,377 		JBrowse link
G Pin1 peptidylprolyl cis/trans isomerase, NIMA-interacting 1 ISO RGD PMID:22713868 RGD:8663430 NCBI chr 8:19,189,408...19,200,785
Ensembl chr 8:19,189,373...19,200,785 		JBrowse link
G Srebf2 sterol regulatory element binding transcription factor 2 ISO RGD PMID:23263379 PMID:22713868 RGD:8663431, RGD:8663430 NCBI chr 7:113,663,202...113,720,850
Ensembl chr 7:113,663,202...113,720,848 		JBrowse link
G Tp53 tumor protein p53 ISO DNA:mutations:exon RGD PMID:19165225 PMID:23759327 PMID:22713868 PMID:23263379 PMID:18772397 More... RGD:2316186, RGD:8693397, RGD:8663430, RGD:8663431, RGD:5490966, RGD:5133242, RGD:4143515 NCBI chr10:54,798,871...54,810,300
Ensembl chr10:54,300,048...54,311,524 		JBrowse link
G Tp63 tumor protein p63 ISO RGD PMID:23263379 PMID:22713868 RGD:8663431, RGD:8663430 NCBI chr11:88,343,647...88,554,543
Ensembl chr11:74,838,859...75,049,398 		JBrowse link
G Tp73 tumor protein p73 ISO RGD PMID:23263379 PMID:22713868 RGD:8663431, RGD:8663430 NCBI chr 5:169,903,801...169,988,075
Ensembl chr 5:164,621,377...164,681,128 		JBrowse link
G Vdr vitamin D receptor ISO RGD PMID:22713868 RGD:8663430 NCBI chr 7:130,864,764...130,916,757
Ensembl chr 7:128,987,981...129,037,677 		JBrowse link
altered SWI/SNF family mediated chromatin remodeling pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Actl6a actin-like 6A ISO RGD PMID:23355908 RGD:8694154 NCBI chr 2:115,492,374...115,508,401
Ensembl chr 2:115,492,285...115,508,401 		JBrowse link
G Arid1a AT-rich interaction domain 1A ISO RGD PMID:23355908 RGD:8694154 NCBI chr 5:151,192,014...151,269,291
Ensembl chr 5:145,908,181...145,985,564 		JBrowse link
G Arid1b AT-rich interaction domain 1B ISO RGD PMID:23355908 RGD:8694154 NCBI chr 1:45,567,991...45,923,644
Ensembl chr 1:45,563,623...45,923,493 		JBrowse link
G Pbrm1 polybromo 1 ISO RGD PMID:23355908 RGD:8694154 NCBI chr16:6,213,507...6,312,895
Ensembl chr16:6,213,300...6,311,780 		JBrowse link
G Smarca4 SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 ISO RGD PMID:23355908 RGD:8694154 NCBI chr 8:28,438,370...28,535,071
Ensembl chr 8:20,167,717...20,258,975 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  pathway 6091
    regulatory pathway 3866
      altered regulatory pathway 79
        altered pathway pertinent to DNA replication and repair, cell cycle, maintenance of genomic integrity, RNA and protein biosynthesis 38
          altered DNA repair pathway + 14
          altered cell cycle pathway + 1
          altered chromatin remodeling/modification pathway + 6
          altered mRNA decay pathway 0
          altered mTOR signaling pathway 0
          altered small non-coding RNA pathway + 0
          altered transcription pathway + 17
          altered translation pathway + 0
paths to the root