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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:HMGA2-HNRNPM (FusionGDB2 ID:36838)

Fusion Gene Summary for HMGA2-HNRNPM

check button Fusion gene summary
Fusion gene informationFusion gene name: HMGA2-HNRNPM
Fusion gene ID: 36838
HgeneTgene
Gene symbol

HMGA2

HNRNPM

Gene ID

8091

4670

Gene namehigh mobility group AT-hook 2heterogeneous nuclear ribonucleoprotein M
SynonymsBABL|HMGI-C|HMGIC|LIPO|STQTL9CEAR|HNRNPM4|HNRPM|HNRPM4|HTGR1|NAGR1|hnRNP M
Cytomap

12q14.3

19p13.2

Type of geneprotein-codingprotein-coding
Descriptionhigh mobility group protein HMGI-CHMGA2/KRT121P fusionhigh-mobility group (nonhistone chromosomal) protein isoform I-Cheterogeneous nuclear ribonucleoprotein MCEA receptorN-acetylglucosamine receptor 1heterogenous nuclear ribonucleoprotein M4hnRNA-binding protein M4
Modification date2020032920200322
UniProtAcc

P52926

P52272

Ensembl transtripts involved in fusion geneENST00000354636, ENST00000393577, 
ENST00000393578, ENST00000403681, 
ENST00000425208, ENST00000536545, 
ENST00000541363, 		ENST00000602219, 
ENST00000325495, ENST00000348943, 
Fusion gene scores* DoF score43 X 25 X 15=1612516 X 16 X 5=1280
# samples 4318
** MAII scorelog2(43/16125*10)=-5.22881869049588
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/1280*10)=-2.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HMGA2 [Title/Abstract] AND HNRNPM [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHMGA2(66221867)-HNRNPM(8520289), # samples:2
Anticipated loss of major functional domain due to fusion event.HMGA2-HNRNPM seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
HMGA2-HNRNPM seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
HMGA2-HNRNPM seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneHMGA2

GO:0000122

negative regulation of transcription by RNA polymerase II

14627817

HgeneHMGA2

GO:0002062

chondrocyte differentiation

21484705

HgeneHMGA2

GO:0006284

base-excision repair

19465398

HgeneHMGA2

GO:0007095

mitotic G2 DNA damage checkpoint

16061642

HgeneHMGA2

GO:0010564

regulation of cell cycle process

14645522

HgeneHMGA2

GO:0010628

positive regulation of gene expression

18832382

HgeneHMGA2

GO:0031052

chromosome breakage

19549901

HgeneHMGA2

GO:0031507

heterochromatin assembly

16901784

HgeneHMGA2

GO:0035978

histone H2A-S139 phosphorylation

16061642

HgeneHMGA2

GO:0035986

senescence-associated heterochromatin focus assembly

16901784

HgeneHMGA2

GO:0035988

chondrocyte proliferation

21484705

HgeneHMGA2

GO:0042769

DNA damage response, detection of DNA damage

19465398

HgeneHMGA2

GO:0043065

positive regulation of apoptotic process

16061642

HgeneHMGA2

GO:0043066

negative regulation of apoptotic process

19465398

HgeneHMGA2

GO:0043392

negative regulation of DNA binding

14645522

HgeneHMGA2

GO:0043922

negative regulation by host of viral transcription

17005673

HgeneHMGA2

GO:0045869

negative regulation of single stranded viral RNA replication via double stranded DNA intermediate

17005673

HgeneHMGA2

GO:0045892

negative regulation of transcription, DNA-templated

18832382

HgeneHMGA2

GO:0045893

positive regulation of transcription, DNA-templated

15225648|15755872|17005673|17324944|17426251

HgeneHMGA2

GO:0045944

positive regulation of transcription by RNA polymerase II

14645522|18832382

HgeneHMGA2

GO:0071158

positive regulation of cell cycle arrest

16061642

HgeneHMGA2

GO:0071902

positive regulation of protein serine/threonine kinase activity

19549901

HgeneHMGA2

GO:0090402

oncogene-induced cell senescence

16901784

HgeneHMGA2

GO:2000648

positive regulation of stem cell proliferation

21484705

HgeneHMGA2

GO:2000679

positive regulation of transcription regulatory region DNA binding

18832382

HgeneHMGA2

GO:2000685

positive regulation of cellular response to X-ray

16061642

HgeneHMGA2

GO:2001022

positive regulation of response to DNA damage stimulus

16061642|19465398

HgeneHMGA2

GO:2001033

negative regulation of double-strand break repair via nonhomologous end joining

19549901

HgeneHMGA2

GO:2001038

regulation of cellular response to drug

16061642


check buttonFusion gene breakpoints across HMGA2 (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 HNRNPM (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-25-2393-01AHMGA2chr12

66221867

+HNRNPMchr19

8520289

+
ChimerDB4OVTCGA-25-2393HMGA2chr12

66221867

+HNRNPMchr19

8520288

+


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Fusion Gene ORF analysis for HMGA2-HNRNPM

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-intronENST00000354636ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
5CDS-intronENST00000354636ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
5CDS-intronENST00000393577ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
5CDS-intronENST00000393577ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
5CDS-intronENST00000393578ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
5CDS-intronENST00000393578ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
5CDS-intronENST00000403681ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
5CDS-intronENST00000403681ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
5CDS-intronENST00000425208ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
5CDS-intronENST00000425208ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
5CDS-intronENST00000536545ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
5CDS-intronENST00000536545ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
5CDS-intronENST00000541363ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
5CDS-intronENST00000541363ENST00000602219HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000354636ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000354636ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000354636ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000354636ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000393577ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000393577ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000393577ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000393577ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000393578ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000393578ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000393578ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000393578ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000403681ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000403681ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000403681ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000403681ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000425208ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000425208ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000425208ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000425208ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000536545ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000536545ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000536545ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000536545ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000541363ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000541363ENST00000325495HMGA2chr12

66221867

+HNRNPMchr19

8520288

+
Frame-shiftENST00000541363ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520289

+
Frame-shiftENST00000541363ENST00000348943HMGA2chr12

66221867

+HNRNPMchr19

8520288

+

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 HMGA2-HNRNPM


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)
HMGA2chr1266221867+HNRNPMchr198520288+4.35E-050.9999565
HMGA2chr1266221867+HNRNPMchr198520288+4.35E-050.9999565
HMGA2chr1266221867+HNRNPMchr198520288+4.35E-050.9999565
HMGA2chr1266221867+HNRNPMchr198520288+4.35E-050.9999565

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 HMGA2-HNRNPM


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/:66221867/:8520289)
- 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
HMGA2

P52926

HNRNPM

P52272

FUNCTION: Functions as a transcriptional regulator. Functions in cell cycle regulation through CCNA2. Plays an important role in chromosome condensation during the meiotic G2/M transition of spermatocytes. Plays a role in postnatal myogenesis, is involved in satellite cell activation (By similarity). Positively regulates IGF2 expression through PLAG1 and in a PLAG1-independent manner (PubMed:28796236). {ECO:0000250|UniProtKB:P52927, ECO:0000269|PubMed:14645522, ECO:0000269|PubMed:28796236}.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.

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 HMGA2-HNRNPM


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 HMGA2-HNRNPM


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 HMGA2-HNRNPM


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 HMGA2-HNRNPM


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