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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:EGFL6-KDM4C (FusionGDB2 ID:25411)

Fusion Gene Summary for EGFL6-KDM4C

check button Fusion gene summary
Fusion gene informationFusion gene name: EGFL6-KDM4C
Fusion gene ID: 25411
HgeneTgene
Gene symbol

EGFL6

KDM4C

Gene ID

25975

23081

Gene nameEGF like domain multiple 6lysine demethylase 4C
SynonymsMAEG|W80GASC1|JHDM3C|JMJD2C|TDRD14C
Cytomap

Xp22.2

9p24.1

Type of geneprotein-codingprotein-coding
Descriptionepidermal growth factor-like protein 6EGF repeat-containing protein 6EGF-like protein 6MAM and EGF domain containingMAM and EGF domains-containing gene proteinlysine-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 14C
Modification date2020031320200329
UniProtAcc

Q8IUX8

Q9H3R0

Ensembl transtripts involved in fusion geneENST00000361306, ENST00000380602, 
ENST00000473826, 		ENST00000535193, 
ENST00000543771, ENST00000381306, 
ENST00000381309, ENST00000442236, 
ENST00000489243, ENST00000536108, 
ENST00000428870, ENST00000401787, 
Fusion gene scores* DoF score3 X 3 X 2=1822 X 22 X 7=3388
# samples 326
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(26/3388*10)=-3.70385034630374
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EGFL6 [Title/Abstract] AND KDM4C [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEGFL6(13618213)-KDM4C(7046861), # samples:1
Anticipated loss of major functional domain due to fusion event.EGFL6-KDM4C seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
EGFL6-KDM4C seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
EGFL6-KDM4C seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
* 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
TgeneKDM4C

GO:0006357

regulation of transcription by RNA polymerase II

17277772

TgeneKDM4C

GO:0033169

histone H3-K9 demethylation

18066052|21914792

TgeneKDM4C

GO:0070544

histone H3-K36 demethylation

21914792


check buttonFusion gene breakpoints across EGFL6 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across KDM4C (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4OVTCGA-24-1562EGFL6chrX

13618213

+KDM4Cchr9

7046861

+


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Fusion Gene ORF analysis for EGFL6-KDM4C

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-shiftENST00000361306ENST00000535193EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000361306ENST00000543771EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000361306ENST00000381306EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000361306ENST00000381309EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000361306ENST00000442236EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
5CDS-intronENST00000361306ENST00000489243EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
5CDS-intronENST00000361306ENST00000536108EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
5CDS-intronENST00000361306ENST00000428870EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
5CDS-intronENST00000361306ENST00000401787EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000380602ENST00000535193EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000380602ENST00000543771EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000380602ENST00000381306EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000380602ENST00000381309EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
Frame-shiftENST00000380602ENST00000442236EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
5CDS-intronENST00000380602ENST00000489243EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
5CDS-intronENST00000380602ENST00000536108EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
5CDS-intronENST00000380602ENST00000428870EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
5CDS-intronENST00000380602ENST00000401787EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-3CDSENST00000473826ENST00000535193EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-3CDSENST00000473826ENST00000543771EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-3CDSENST00000473826ENST00000381306EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-3CDSENST00000473826ENST00000381309EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-3CDSENST00000473826ENST00000442236EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-intronENST00000473826ENST00000489243EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-intronENST00000473826ENST00000536108EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-intronENST00000473826ENST00000428870EGFL6chrX

13618213

+KDM4Cchr9

7046861

+
intron-intronENST00000473826ENST00000401787EGFL6chrX

13618213

+KDM4Cchr9

7046861

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for EGFL6-KDM4C


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
EGFL6chrX13618213+KDM4Cchr97046861+0.263152270.7368477
EGFL6chrX13618213+KDM4Cchr97046861+0.263152270.7368477

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for EGFL6-KDM4C


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
EGFL6

Q8IUX8

KDM4C

Q9H3R0

FUNCTION: May bind integrin alpha-8/beta-1 and play a role in hair follicle morphogenesis. Promotes matrix assembly (By similarity). {ECO:0000250}.FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. {ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:28262558}.

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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Fusion Gene Sequence for EGFL6-KDM4C


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for EGFL6-KDM4C


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


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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Related Drugs for EGFL6-KDM4C


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for EGFL6-KDM4C


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneKDM4CC0004565Melanoma, B161CTD_human
TgeneKDM4CC0009075Melanoma, Cloudman S911CTD_human
TgeneKDM4CC0018598Melanoma, Harding-Passey1CTD_human
TgeneKDM4CC0025149Medulloblastoma1CTD_human
TgeneKDM4CC0025202melanoma1CTD_human
TgeneKDM4CC0025205Melanoma, Experimental1CTD_human
TgeneKDM4CC0079772T-Cell Lymphoma1CTD_human
TgeneKDM4CC0205833Medullomyoblastoma1CTD_human
TgeneKDM4CC0236663Alcohol withdrawal syndrome1PSYGENET
TgeneKDM4CC0278510Childhood Medulloblastoma1CTD_human
TgeneKDM4CC0278876Adult Medulloblastoma1CTD_human
TgeneKDM4CC0751291Desmoplastic Medulloblastoma1CTD_human
TgeneKDM4CC1275668Melanotic medulloblastoma1CTD_human