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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:EHMT1-NELFB

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EHMT1-NELFB
FusionPDB ID: 25585
FusionGDB2.0 ID: 25585
HgeneTgene
Gene symbol

EHMT1

NELFB

Gene ID

79813

25920

Gene nameeuchromatic histone lysine methyltransferase 1negative elongation factor complex member B
SynonymsEHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1DCOBRA1|NELF-B
Cytomap

9q34.3

9q34.3

Type of geneprotein-codingprotein-coding
Descriptionhistone-lysine N-methyltransferase EHMT1EHMT1 intronic transcript 1G9a-like protein 1H3-K9-HMTase 5euchromatic histone-lysine N-methyltransferase 1histone H3-K9 methyltransferase 5histone-lysine N-methyltransferase, H3 lysine-9 specific 5lysine N-mnegative elongation factor Bcofactor of BRCA1negative elongation factor protein B
Modification date2020031320200313
UniProtAcc

Q9H9B1

Q8WX92

Ensembl transtripts involved in fusion geneENST idsENST00000371394, ENST00000334856, 
ENST00000460843, ENST00000462484, 
ENST00000343053, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 9 X 8=108010 X 8 X 4=320
# samples 2010
** MAII scorelog2(20/1080*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/320*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: EHMT1 [Title/Abstract] AND NELFB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EHMT1(140513501)-NELFB(140157489), # samples:1
Anticipated loss of major functional domain due to fusion event.EHMT1-NELFB seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
EHMT1-NELFB seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgeneEHMT1

GO:0006325

chromatin organization

12004135

HgeneEHMT1

GO:0016571

histone methylation

12004135

HgeneEHMT1

GO:0018027

peptidyl-lysine dimethylation

20118233


check buttonFusion gene breakpoints across EHMT1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4STADTCGA-FP-8631-01AEHMT1chr9

140513501

+NELFBchr9

140157489

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000462484EHMT1chr9140513501+ENST00000343053NELFBchr9140157489+182258221203393
ENST00000460843EHMT1chr9140513501+ENST00000343053NELFBchr9140157489+181248121193393

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
ENST00000462484ENST00000343053EHMT1chr9140513501+NELFBchr9140157489+0.0117683130.9882317
ENST00000460843ENST00000343053EHMT1chr9140513501+NELFBchr9140157489+0.0122417250.9877582

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>25585_25585_1_EHMT1-NELFB_EHMT1_chr9_140513501_ENST00000460843_NELFB_chr9_140157489_ENST00000343053_length(amino acids)=393AA_BP=12
MRARAMAAADAEVVQRLTRMVGKNVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMSLHDLDVGEICTVDPCHKFTWCLDACIRERFVDS
KRARELQGFLDGVKKGQEQVLGDLSMILCDPFAINTLALSTVRHLQELVGQETLPRDSPDLLLLLRLLALGQGAWDMIDSQVFKEPKMEV
ELITRFLPMLMSFLVDDYTFNVDQKLPAEEKAPVSYPNTLPESFTKFLQEQRMACEVGLYYVLHITKQRNKNALLRLLPGLVETFGDLAF
GDIFLHLLTGNLALLADEFALEDFCSSLFDGFFLTASPRKENVHRHALRLLIHLHPRVAPSKLEALQKALEPTGQSGEAVKELYSQLGEK

--------------------------------------------------------------

>25585_25585_2_EHMT1-NELFB_EHMT1_chr9_140513501_ENST00000462484_NELFB_chr9_140157489_ENST00000343053_length(amino acids)=393AA_BP=12
MRARAMAAADAEVVQRLTRMVGKNVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMSLHDLDVGEICTVDPCHKFTWCLDACIRERFVDS
KRARELQGFLDGVKKGQEQVLGDLSMILCDPFAINTLALSTVRHLQELVGQETLPRDSPDLLLLLRLLALGQGAWDMIDSQVFKEPKMEV
ELITRFLPMLMSFLVDDYTFNVDQKLPAEEKAPVSYPNTLPESFTKFLQEQRMACEVGLYYVLHITKQRNKNALLRLLPGLVETFGDLAF
GDIFLHLLTGNLALLADEFALEDFCSSLFDGFFLTASPRKENVHRHALRLLIHLHPRVAPSKLEALQKALEPTGQSGEAVKELYSQLGEK

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Fusion Protein Functional Features


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/chr9:140513501/chr9:140157489)
- 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
EHMT1

Q9H9B1

NELFB

Q8WX92

FUNCTION: Histone methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting HP1 proteins to methylated histones. Also weakly methylates 'Lys-27' of histone H3 (H3K27me). Also required for DNA methylation, the histone methyltransferase activity is not required for DNA methylation, suggesting that these 2 activities function independently. Probably targeted to histone H3 by different DNA-binding proteins like E2F6, MGA, MAX and/or DP1. During G0 phase, it probably contributes to silencing of MYC- and E2F-responsive genes, suggesting a role in G0/G1 transition in cell cycle. In addition to the histone methyltransferase activity, also methylates non-histone proteins: mediates dimethylation of 'Lys-373' of p53/TP53. Represses the expression of mitochondrial function-related genes, perhaps by occupying their promoter regions, working in concert with probable chromatin reader BAZ2B (By similarity). {ECO:0000250|UniProtKB:Q5DW34, ECO:0000269|PubMed:12004135, ECO:0000269|PubMed:20118233}.FUNCTION: Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II (PubMed:12612062). The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex (PubMed:10199401). May be able to induce chromatin unfolding (PubMed:11739404). Essential for early embryogenesis; plays an important role in maintaining the undifferentiated state of embryonic stem cells (ESCs) by preventing unscheduled expression of developmental genes (By similarity). Plays a key role in establishing the responsiveness of stem cells to developmental cues; facilitates plasticity and cell fate commitment in ESCs by establishing the appropriate expression level of signaling molecules (By similarity). Supports the transcription of genes involved in energy metabolism in cardiomyocytes; facilitates the association of transcription initiation factors with the promoters of the metabolism-related genes (By similarity). {ECO:0000250|UniProtKB:Q8C4Y3, ECO:0000269|PubMed:10199401, ECO:0000269|PubMed:11739404, ECO:0000269|PubMed:12612062}.; FUNCTION: (Microbial infection) The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II (PubMed:23884411). In vitro, binds weakly to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1 (PubMed:23884411). {ECO:0000269|PubMed:23884411}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+1171292_12950826.0Compositional biasNote=Poly-Ala
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117406_4090826.0Compositional biasNote=Poly-Glu
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117442_4490826.0Compositional biasNote=Poly-Arg
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+1271292_12957.01299.0Compositional biasNote=Poly-Ala
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127406_4097.01299.0Compositional biasNote=Poly-Glu
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127442_4497.01299.0Compositional biasNote=Poly-Arg
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+1161292_12957.0809.0Compositional biasNote=Poly-Ala
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116406_4097.0809.0Compositional biasNote=Poly-Glu
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116442_4497.0809.0Compositional biasNote=Poly-Arg
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+1171060_11230826.0DomainPre-SET
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+1171126_12430826.0DomainSET
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+1271060_11237.01299.0DomainPre-SET
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+1271126_12437.01299.0DomainSET
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+1161060_11237.0809.0DomainPre-SET
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+1161126_12437.0809.0DomainSET
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+1171136_11380826.0RegionNote=S-adenosyl-L-methionine binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+1171200_12010826.0RegionNote=S-adenosyl-L-methionine binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117905_9070826.0RegionNote=Histone H3K9me binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+1271136_11387.01299.0RegionNote=S-adenosyl-L-methionine binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+1271200_12017.01299.0RegionNote=S-adenosyl-L-methionine binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127905_9077.01299.0RegionNote=Histone H3K9me binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+1161136_11387.0809.0RegionNote=S-adenosyl-L-methionine binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+1161200_12017.0809.0RegionNote=S-adenosyl-L-methionine binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116905_9077.0809.0RegionNote=Histone H3K9me binding
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117737_7660826.0RepeatNote=ANK 1
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117772_8010826.0RepeatNote=ANK 2
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117805_8340826.0RepeatNote=ANK 3
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117838_8680826.0RepeatNote=ANK 4
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117872_9010826.0RepeatNote=ANK 5
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117905_9340826.0RepeatNote=ANK 6
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117938_9670826.0RepeatNote=ANK 7
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+117971_10040826.0RepeatNote=ANK 8
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127737_7667.01299.0RepeatNote=ANK 1
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127772_8017.01299.0RepeatNote=ANK 2
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127805_8347.01299.0RepeatNote=ANK 3
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127838_8687.01299.0RepeatNote=ANK 4
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127872_9017.01299.0RepeatNote=ANK 5
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127905_9347.01299.0RepeatNote=ANK 6
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127938_9677.01299.0RepeatNote=ANK 7
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+127971_10047.01299.0RepeatNote=ANK 8
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116737_7667.0809.0RepeatNote=ANK 1
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116772_8017.0809.0RepeatNote=ANK 2
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116805_8347.0809.0RepeatNote=ANK 3
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116838_8687.0809.0RepeatNote=ANK 4
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116872_9017.0809.0RepeatNote=ANK 5
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116905_9347.0809.0RepeatNote=ANK 6
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116938_9677.0809.0RepeatNote=ANK 7
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+116971_10047.0809.0RepeatNote=ANK 8


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
EHMT1
NELFB


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+1171162_11810826.0histone H3
HgeneEHMT1chr9:140513501chr9:140157489ENST00000334856+1171242_12450826.0histone H3
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+1271162_11817.01299.0histone H3
HgeneEHMT1chr9:140513501chr9:140157489ENST00000460843+1271242_12457.01299.0histone H3
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+1161162_11817.0809.0histone H3
HgeneEHMT1chr9:140513501chr9:140157489ENST00000462484+1161242_12457.0809.0histone H3


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Related Drugs to EHMT1-NELFB


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to EHMT1-NELFB


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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