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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-SOX5 (FusionGDB2 ID:36857)

Fusion Gene Summary for HMGA2-SOX5

check button Fusion gene summary
Fusion gene informationFusion gene name: HMGA2-SOX5
Fusion gene ID: 36857
HgeneTgene
Gene symbol

HMGA2

SOX5

Gene ID

8091

6660

Gene namehigh mobility group AT-hook 2SRY-box transcription factor 5
SynonymsBABL|HMGI-C|HMGIC|LIPO|STQTL9L-SOX5|L-SOX5B|L-SOX5F|LAMSHF
Cytomap

12q14.3

12p12.1

Type of geneprotein-codingprotein-coding
Descriptionhigh mobility group protein HMGI-CHMGA2/KRT121P fusionhigh-mobility group (nonhistone chromosomal) protein isoform I-Ctranscription factor SOX-5SRY (sex determining region Y)-box 5SRY-box 5
Modification date2020032920200313
UniProtAcc

P52926

.
Ensembl transtripts involved in fusion geneENST00000403681, ENST00000354636, 
ENST00000393577, ENST00000393578, 
ENST00000425208, ENST00000536545, 
ENST00000541363, 		ENST00000309359, 
ENST00000381381, ENST00000396007, 
ENST00000441133, ENST00000451604, 
ENST00000536850, ENST00000537393, 
ENST00000541536, ENST00000541847, 
ENST00000545921, ENST00000546136, 
Fusion gene scores* DoF score43 X 25 X 15=1612516 X 19 X 9=2736
# samples 4318
** MAII scorelog2(43/16125*10)=-5.22881869049588
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/2736*10)=-3.92599941855622
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HMGA2 [Title/Abstract] AND SOX5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint
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
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

TgeneSOX5

GO:0032332

positive regulation of chondrocyte differentiation

21401405

TgeneSOX5

GO:0061036

positive regulation of cartilage development

21401405

TgeneSOX5

GO:0071560

cellular response to transforming growth factor beta stimulus

21401405

TgeneSOX5

GO:2000741

positive regulation of mesenchymal stem cell differentiation

21401405


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 SOX5 (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
ChimerKB4..HMGA2chr12

66218239

+SOX5chr12

66218239

-


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Fusion Gene ORF analysis for HMGA2-SOX5

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
5UTR-intronENST00000403681ENST00000309359HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000381381HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000396007HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000441133HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000451604HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000536850HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000537393HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000541536HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000541847HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000545921HMGA2chr12

66218239

+SOX5chr12

66218239

-
5UTR-intronENST00000403681ENST00000546136HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000309359HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000381381HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000396007HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000441133HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000451604HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000536850HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000537393HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000541536HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000541847HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000545921HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000354636ENST00000546136HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000309359HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000381381HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000396007HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000441133HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000451604HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000536850HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000537393HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000541536HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000541847HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000545921HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393577ENST00000546136HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000309359HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000381381HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000396007HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000441133HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000451604HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000536850HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000537393HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000541536HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000541847HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000545921HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000393578ENST00000546136HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000309359HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000381381HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000396007HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000441133HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000451604HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000536850HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000537393HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000541536HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000541847HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000545921HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000425208ENST00000546136HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000309359HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000381381HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000396007HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000441133HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000451604HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000536850HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000537393HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000541536HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000541847HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000545921HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000536545ENST00000546136HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000309359HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000381381HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000396007HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000441133HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000451604HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000536850HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000537393HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000541536HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000541847HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000545921HMGA2chr12

66218239

+SOX5chr12

66218239

-
intron-intronENST00000541363ENST00000546136HMGA2chr12

66218239

+SOX5chr12

66218239

-

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-SOX5


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)

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 HMGA2-SOX5


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/:/:)
- 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

.
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: 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 HMGA2-SOX5


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-SOX5


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-SOX5


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-SOX5


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