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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:CARM1-KLF11 (FusionGDB2 ID:HG10498TG8462)

Fusion Gene Summary for CARM1-KLF11

check button Fusion gene summary
Fusion gene informationFusion gene name: CARM1-KLF11
Fusion gene ID: hg10498tg8462
HgeneTgene
Gene symbol

CARM1

KLF11

Gene ID

10498

8462

Gene namecoactivator associated arginine methyltransferase 1Kruppel like factor 11
SynonymsPRMT4FKLF|FKLF1|MODY7|TIEG2|Tieg3
Cytomap('CARM1')('KLF11')

19p13.2

2p25.1

Type of geneprotein-codingprotein-coding
Descriptionhistone-arginine methyltransferase CARM1protein arginine N-methyltransferase 4Krueppel-like factor 11TGFB-inducible early growth response protein 2TIEG-2transforming growth factor-beta-inducible early growth response protein 2
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000327064, ENST00000344150, 
Fusion gene scores* DoF score14 X 10 X 10=14002 X 2 X 2=8
# samples 202
** MAII scorelog2(20/1400*10)=-2.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: CARM1 [Title/Abstract] AND KLF11 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCARM1(10982598)-KLF11(10187777), # samples:2
Anticipated loss of major functional domain due to fusion event.CARM1-KLF11 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CARM1-KLF11 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CARM1-KLF11 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CARM1-KLF11 seems lost the major protein functional domain in Tgene partner, which is a transcription 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
HgeneCARM1

GO:0016571

histone methylation

19405910

TgeneKLF11

GO:0000083

regulation of transcription involved in G1/S transition of mitotic cell cycle

21171965

TgeneKLF11

GO:0000122

negative regulation of transcription by RNA polymerase II

21171965

TgeneKLF11

GO:0008285

negative regulation of cell proliferation

21171965

TgeneKLF11

GO:0043065

positive regulation of apoptotic process

21171965



check button Fusion gene information
* 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
ChimerDB4COADTCGA-CM-6167-01ACARM1chr19

10982598

-KLF11chr2

10187777

+
ChimerDB4COADTCGA-CM-6167-01ACARM1chr19

10982598

+KLF11chr2

10187777

+


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Fusion Gene ORF analysis for CARM1-KLF11

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-shiftENST00000327064ENST00000305883CARM1chr19

10982598

+KLF11chr2

10187777

+
Frame-shiftENST00000327064ENST00000535335CARM1chr19

10982598

+KLF11chr2

10187777

+
Frame-shiftENST00000327064ENST00000540845CARM1chr19

10982598

+KLF11chr2

10187777

+
Frame-shiftENST00000344150ENST00000305883CARM1chr19

10982598

+KLF11chr2

10187777

+
Frame-shiftENST00000344150ENST00000535335CARM1chr19

10982598

+KLF11chr2

10187777

+
Frame-shiftENST00000344150ENST00000540845CARM1chr19

10982598

+KLF11chr2

10187777

+

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 CARM1-KLF11


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)
CARM1chr1910982598+KLF11chr210187776+5.15E-151
CARM1chr1910982598+KLF11chr210187776+5.15E-151


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.
genomic feature of top 1%

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Fusion Protein Features for CARM1-KLF11


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:10982598/:10187777)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 CARM1-KLF11


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 CARM1-KLF11


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 CARM1-KLF11


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 CARM1-KLF11


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCARM1C0030246Pustulosis of Palms and Soles1CTD_human
HgeneCARM1C0033860Psoriasis1CTD_human
TgeneC0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneC0019209Hepatomegaly1CTD_human
TgeneC0342276Maturity onset diabetes mellitus in young1GENOMICS_ENGLAND;ORPHANET
TgeneC1864839MATURITY-ONSET DIABETES OF THE YOUNG, TYPE 7 (disorder)1CTD_human;GENOMICS_ENGLAND;UNIPROT