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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 18446

FusionGeneSummary for KDM4A_RYBP

check button Fusion gene summary
Fusion gene informationFusion gene name: KDM4A_RYBP
Fusion gene ID: 18446
HgeneTgene
Gene symbol

KDM4A

RYBP

Gene ID

9682

23429

Gene namelysine demethylase 4ARING1 and YY1 binding protein
SynonymsJHDM3A|JMJD2|JMJD2A|TDRD14AAAP1|APAP-1|DEDAF|YEAF1
Cytomap

1p34.2-p34.1

3p13

Type of geneprotein-codingprotein-coding
Descriptionlysine-specific demethylase 4AjmjC domain-containing histone demethylation protein 3Ajumonji C domain-containing histone demethylase 3Ajumonji domain containing 2jumonji domain containing 2Ajumonji domain-containing protein 2Alysine (K)-specific demRING1 and YY1-binding proteinDED-associated factorYY1 and E4TF1 associated factor 1apoptin-associating protein 1death effector domain-associated factorring1 interactor RYBP
Modification date2018052320180519
UniProtAcc

O75164

Q8N488

Ensembl transtripts involved in fusion geneENST00000372396, ENST00000463151, 
ENST00000477973, 
Fusion gene scores* DoF score13 X 12 X 9=14041 X 1 X 1=1
# samples 131
** MAII scorelog2(13/1404*10)=-3.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: KDM4A [Title/Abstract] AND RYBP [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneKDM4A

GO:0016577

histone demethylation

16024779

HgeneKDM4A

GO:0045892

negative regulation of transcription, DNA-templated

16024779

HgeneKDM4A

GO:0070544

histone H3-K36 demethylation

21914792

TgeneRYBP

GO:0035518

histone H2A monoubiquitination

16943429


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLUADTCGA-78-7153-01AKDM4Achr1

44149475

+RYBPchr3

72428578

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shitENST00000372396ENST00000477973KDM4Achr1

44149475

+RYBPchr3

72428578

-
intron-3CDSENST00000463151ENST00000477973KDM4Achr1

44149475

+RYBPchr3

72428578

-

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FusionProtFeatures for KDM4A_RYBP


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KDM4A

O75164

RYBP

Q8N488

Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a centralrole in histone code (PubMed:26741168). Does not demethylatehistone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylatestrimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has noactivity on mono- and dimethylated residues. Demethylation of Lysresidue generates formaldehyde and succinate. Participates intranscriptional repression of ASCL2 and E2F-responsive promotersvia the recruitment of histone deacetylases and NCOR1,respectively. {ECO:0000269|PubMed:16024779,ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:26741168}. Isoform 2: Crucial for muscle differentiation, promotestranscriptional activation of the Myog gene by directing theremoval of repressive chromatin marks at its promoter. Lacks theN-terminal demethylase domain. {ECO:0000269|PubMed:21694756}. Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain thetranscriptionally repressive state of many genes, including Hoxgenes, throughout development. PcG PRC1-like complex acts viachromatin remodeling and modification of histones; it mediatesmonoubiquitination of histone H2A 'Lys-119', rendering chromatinheritably changed in its expressibility (PubMed:25519132).Component of a PRC1-like complex that mediates monoubiquitinationof histone H2A 'Lys-119' on the X chromosome and is required fornormal silencing of one copy of the X chromosome in XX females.May stimulate ubiquitination of histone H2A 'Lys-119' byrecruiting the complex to target sites (By similarity). Inhibitsubiquitination and subsequent degradation of TP53, and therebyplays a role in regulating transcription of TP53 target genes(PubMed:19098711). May also regulate the ubiquitin-mediatedproteasomal degradation of other proteins like FANK1 to regulateapoptosis (PubMed:14765135, PubMed:27060496). May be implicated inthe regulation of the transcription as a repressor of thetranscriptional activity of E4TF1 (PubMed:11953439). May bind toDNA (By similarity). {ECO:0000250|UniProtKB:Q8CCI5,ECO:0000269|PubMed:11953439, ECO:0000269|PubMed:14765135,ECO:0000269|PubMed:19098711, ECO:0000269|PubMed:27060496}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for KDM4A_RYBP


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for KDM4A_RYBP


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
KDM4ANCOR1, WDR48, KDM4A, KDM4C, HIST1H3A, HDAC1, HDAC3, RB1, AR, WAS, HIST1H4A, RNF8, RNF168, H3F3A, CUL1, FBXL4, MOV10, NXF1, CAPZA1, EPHB2, ZNF131, ZNF414, CCL22, STK11, KDM4B, ABHD5RYBPE2F6, RING1, CBX2, YY1, E2F2, E2F3, E2F4, CASP10, FADD, ABL1, MDM2, TP53, BCOR, PCGF1, RNF2, SOCS2, ZFP42, ELAVL1, PCGF2, PCGF3, BMI1, PCGF5, PCGF6, L3MBTL2, CBX3, TFDP1, WDR5, MGA, SKP1, BCORL1, KDM2B, USP7, FBRS, FBRSL1, CSNK2A1, CSNK2A2, CSNK2B, GABPB1, GABPB2, EED, MORC4, ATF7IP, HERC2, AUTS2, HSPB1, CRK, NOS1AP, MAPK8IP2, FANK1, DDX5, CASP8, MLLT1, YAF2, TFDP2, HDAC1, DCAF7, TRIM25


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for KDM4A_RYBP


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for KDM4A_RYBP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource