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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: 18477

FusionGeneSummary for KDM4C_RFX3

check button Fusion gene summary
Fusion gene informationFusion gene name: KDM4C_RFX3
Fusion gene ID: 18477
HgeneTgene
Gene symbol

KDM4C

RFX3

Gene ID

23081

5991

Gene namelysine demethylase 4Cregulatory factor X3
SynonymsGASC1|JHDM3C|JMJD2C|TDRD14C-
Cytomap

9p24.1

9p24.2

Type of geneprotein-codingprotein-coding
Descriptionlysine-specific demethylase 4CJmjC domain-containing histone demethylation protein 3Cgene amplified in squamous cell carcinoma 1 proteinjumonji domain-containing protein 2Clysine (K)-specific demethylase 4Ctudor domain containing 14Ctranscription factor RFX3DNA binding protein RFX3regulatory factor X, 3 (influences HLA class II expression)
Modification date2018052320180523
UniProtAcc

Q9H3R0

P48380

Ensembl transtripts involved in fusion geneENST00000535193, ENST00000543771, 
ENST00000381306, ENST00000381309, 
ENST00000442236, ENST00000489243, 
ENST00000536108, ENST00000428870, 
ENST00000401787, 
ENST00000382004, 
ENST00000358730, ENST00000302303, 
ENST00000381984, 
Fusion gene scores* DoF score11 X 8 X 10=8803 X 3 X 2=18
# samples 122
** MAII scorelog2(12/880*10)=-2.87446911791614
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/18*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: KDM4C [Title/Abstract] AND RFX3 [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
HgeneKDM4C

GO:0006357

regulation of transcription by RNA polymerase II

17277772

HgeneKDM4C

GO:0033169

histone H3-K9 demethylation

18066052|21914792

HgeneKDM4C

GO:0070544

histone H3-K36 demethylation

21914792

TgeneRFX3

GO:0045892

negative regulation of transcription, DNA-templated

12411430

TgeneRFX3

GO:0045893

positive regulation of transcription, DNA-templated

20148032


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
TCGARVKIRCTCGA-B0-4696-01AKDM4Cchr9

6805774

+RFX3chr9

3225280

-
* 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-shitENST00000535193ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000535193ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000535193ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000535193ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
Frame-shitENST00000543771ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000543771ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000543771ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000543771ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
Frame-shitENST00000381306ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381306ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381306ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381306ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
Frame-shitENST00000381309ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381309ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381309ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381309ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-3CDSENST00000442236ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000442236ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000442236ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000442236ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
3UTR-3CDSENST00000489243ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
3UTR-intronENST00000489243ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
3UTR-intronENST00000489243ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
3UTR-intronENST00000489243ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5UTR-3CDSENST00000536108ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5UTR-intronENST00000536108ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5UTR-intronENST00000536108ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5UTR-intronENST00000536108ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-3CDSENST00000428870ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000428870ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000428870ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000428870ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
Frame-shitENST00000401787ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000401787ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000401787ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000401787ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-

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FusionProtFeatures for KDM4C_RFX3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KDM4C

Q9H3R0

RFX3

P48380


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 KDM4C_RFX3


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 KDM4C_RFX3


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
KDM4CKDM4A, KDM4C, HIST1H3A, H3F3A, PPARG, HDAC1, HDAC3, HIST2H3C, SHMT2, MOV10, NXF1, TRIM25RFX3TRAF2, RFX6, RFX4, BIN1, CREB1, EWSR1, IRF6, PKNOX1, SOX2, FHL2, FHL3, TRIP6, SEC63, PABPC5, FOXJ1, FOXJ2, FOXN3, FAM188A, IGSF8, RFX1, HDAC1, XYLT2, RTCB, MTA2, PTOV1, DDX1, TBC1D32, VPS45, TAF6L, MBD2, CDK20, ACAD9, HDAC2, TMED4, CFAP20, PLK1


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 KDM4C_RFX3


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 KDM4C_RFX3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKDM4CC0025149Medulloblastoma1CTD_human
HgeneKDM4CC0236663Alcohol withdrawal syndrome1PSYGENET
TgeneRFX3C0037274Dermatologic disorders1CTD_human
TgeneRFX3C0311375Arsenic Poisoning1CTD_human