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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:HNRNPM-KDM4B (FusionGDB2 ID:37278)

Fusion Gene Summary for HNRNPM-KDM4B

check button Fusion gene summary
Fusion gene informationFusion gene name: HNRNPM-KDM4B
Fusion gene ID: 37278
HgeneTgene
Gene symbol

HNRNPM

KDM4B

Gene ID

4670

23030

Gene nameheterogeneous nuclear ribonucleoprotein Mlysine demethylase 4B
SynonymsCEAR|HNRNPM4|HNRPM|HNRPM4|HTGR1|NAGR1|hnRNP MJMJD2B|TDRD14B
Cytomap

19p13.2

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionheterogeneous nuclear ribonucleoprotein MCEA receptorN-acetylglucosamine receptor 1heterogenous nuclear ribonucleoprotein M4hnRNA-binding protein M4lysine-specific demethylase 4BjmjC domain-containing histone demethylation protein 3Bjumonji domain containing 2Bjumonji domain-containing protein 2Blysine (K)-specific demethylase 4Btudor domain containing 14B
Modification date2020032220200313
UniProtAcc

P52272

O94953

Ensembl transtripts involved in fusion geneENST00000325495, ENST00000348943, 
ENST00000602219, 		ENST00000159111, 
ENST00000381759, ENST00000536461, 
ENST00000592175, 
Fusion gene scores* DoF score16 X 12 X 10=192010 X 14 X 9=1260
# samples 1916
** MAII scorelog2(19/1920*10)=-3.33703498727757
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1260*10)=-2.97727992349992
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HNRNPM [Title/Abstract] AND KDM4B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHNRNPM(8539128)-KDM4B(5016268), # samples:1
HNRNPM(8539128)-KDM4B(5016267), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneKDM4B

GO:0033169

histone H3-K9 demethylation

21914792

TgeneKDM4B

GO:0070544

histone H3-K36 demethylation

21914792


check buttonFusion gene breakpoints across HNRNPM (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 KDM4B (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-23-2078-01AHNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
ChimerDB4OVTCGA-23-2078HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+


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Fusion Gene ORF analysis for HNRNPM-KDM4B

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
5CDS-5UTRENST00000325495ENST00000159111HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
5CDS-5UTRENST00000325495ENST00000159111HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
5CDS-5UTRENST00000325495ENST00000381759HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
5CDS-5UTRENST00000325495ENST00000381759HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
5CDS-5UTRENST00000348943ENST00000159111HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
5CDS-5UTRENST00000348943ENST00000159111HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
5CDS-5UTRENST00000348943ENST00000381759HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
5CDS-5UTRENST00000348943ENST00000381759HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
5CDS-intronENST00000325495ENST00000536461HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
5CDS-intronENST00000325495ENST00000536461HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
5CDS-intronENST00000325495ENST00000592175HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
5CDS-intronENST00000325495ENST00000592175HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
5CDS-intronENST00000348943ENST00000536461HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
5CDS-intronENST00000348943ENST00000536461HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
5CDS-intronENST00000348943ENST00000592175HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
5CDS-intronENST00000348943ENST00000592175HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
intron-5UTRENST00000602219ENST00000159111HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
intron-5UTRENST00000602219ENST00000159111HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
intron-5UTRENST00000602219ENST00000381759HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
intron-5UTRENST00000602219ENST00000381759HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
intron-intronENST00000602219ENST00000536461HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
intron-intronENST00000602219ENST00000536461HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+
intron-intronENST00000602219ENST00000592175HNRNPMchr19

8539128

+KDM4Bchr19

5016268

+
intron-intronENST00000602219ENST00000592175HNRNPMchr19

8539128

+KDM4Bchr19

5016267

+

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 HNRNPM-KDM4B


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)
HNRNPMchr198539128+KDM4Bchr195016267+0.0003347750.99966526
HNRNPMchr198539128+KDM4Bchr195016267+0.0003347750.99966526
HNRNPMchr198539128+KDM4Bchr195016267+0.0003347750.99966526
HNRNPMchr198539128+KDM4Bchr195016267+0.0003347750.99966526

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.
genomic feature of top 1%

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Fusion Protein Features for HNRNPM-KDM4B


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/:8539128/:5016268)
- 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
HNRNPM

P52272

KDM4B

O94953

FUNCTION: Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. 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 HNRNPM-KDM4B


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 HNRNPM-KDM4B


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 HNRNPM-KDM4B


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 HNRNPM-KDM4B


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