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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:CHD9-MMP2 (FusionGDB2 ID:HG80205TG4313)

Fusion Gene Summary for CHD9-MMP2

check button Fusion gene summary
Fusion gene informationFusion gene name: CHD9-MMP2
Fusion gene ID: hg80205tg4313
HgeneTgene
Gene symbol

CHD9

MMP2

Gene ID

80205

4313

Gene namechromodomain helicase DNA binding protein 9matrix metallopeptidase 2
SynonymsAD013|CHD-9|CReMM|KISH2|PRIC320CLG4|CLG4A|MMP-2|MMP-II|MONA|TBE-1
Cytomap('CHD9')('MMP2')

16q12.2

16q12.2

Type of geneprotein-codingprotein-coding
Descriptionchromodomain-helicase-DNA-binding protein 9ATP-dependent helicase CHD9PPAR-alpha-interacting complex protein 320 kDaPPAR{gamma}-interacting cofactor 320 kDachromatin remodeling factor CHROM1chromatin-related mesenchymal modulatorciprofibrate bound p72 kDa type IV collagenasecollagenase type IV-Amatrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)matrix metalloproteinase-2matrix metalloproteinase-IIneutrophil gelatinase
Modification date2020032020200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000447540, ENST00000566029, 
ENST00000398510, ENST00000564582, 
ENST00000564845, 
Fusion gene scores* DoF score13 X 9 X 6=7027 X 7 X 4=196
# samples 137
** MAII scorelog2(13/702*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/196*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHD9 [Title/Abstract] AND MMP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHD9(53088989)-MMP2(55498464), # 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
TgeneMMP2

GO:0006508

proteolysis

15863497



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
ChimerDB4MESOTCGA-MQ-A4LJ-01ACHD9chr16

53088989

+MMP2chr16

55498464

+


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Fusion Gene ORF analysis for CHD9-MMP2

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-5UTRENST00000447540ENST00000570308CHD9chr16

53088989

+MMP2chr16

55498464

+
5UTR-5UTRENST00000566029ENST00000570308CHD9chr16

53088989

+MMP2chr16

55498464

+
5UTR-intronENST00000447540ENST00000219070CHD9chr16

53088989

+MMP2chr16

55498464

+
5UTR-intronENST00000447540ENST00000437642CHD9chr16

53088989

+MMP2chr16

55498464

+
5UTR-intronENST00000447540ENST00000543485CHD9chr16

53088989

+MMP2chr16

55498464

+
5UTR-intronENST00000566029ENST00000219070CHD9chr16

53088989

+MMP2chr16

55498464

+
5UTR-intronENST00000566029ENST00000437642CHD9chr16

53088989

+MMP2chr16

55498464

+
5UTR-intronENST00000566029ENST00000543485CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-5UTRENST00000398510ENST00000570308CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-5UTRENST00000564582ENST00000570308CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-5UTRENST00000564845ENST00000570308CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000398510ENST00000219070CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000398510ENST00000437642CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000398510ENST00000543485CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000564582ENST00000219070CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000564582ENST00000437642CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000564582ENST00000543485CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000564845ENST00000219070CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000564845ENST00000437642CHD9chr16

53088989

+MMP2chr16

55498464

+
intron-intronENST00000564845ENST00000543485CHD9chr16

53088989

+MMP2chr16

55498464

+

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 CHD9-MMP2


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)
CHD9chr1653088989+MMP2chr1655498463+0.0002896740.99971026
CHD9chr1653088989+MMP2chr1655498463+0.0002896740.99971026


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 CHD9-MMP2


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/:53088989/:55498464)
- 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 CHD9-MMP2


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 CHD9-MMP2


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 CHD9-MMP2


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 CHD9-MMP2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0027627Neoplasm Metastasis6CTD_human
TgeneC0027626Neoplasm Invasiveness4CTD_human
TgeneC1850155TORG-WINCHESTER SYNDROME3CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0006142Malignant neoplasm of breast2CTD_human
TgeneC0006663Calcinosis2CTD_human
TgeneC0009402Colorectal Carcinoma2CTD_human;UNIPROT
TgeneC0009404Colorectal Neoplasms2CTD_human
TgeneC0023890Liver Cirrhosis2CTD_human
TgeneC0023893Liver Cirrhosis, Experimental2CTD_human
TgeneC0027051Myocardial Infarction2CTD_human
TgeneC0239946Fibrosis, Liver2CTD_human
TgeneC0263628Tumoral calcinosis2CTD_human
TgeneC0376634Craniofacial Abnormalities2CTD_human
TgeneC0521174Microcalcification2CTD_human
TgeneC0678222Breast Carcinoma2CTD_human
TgeneC1257931Mammary Neoplasms, Human2CTD_human
TgeneC1458155Mammary Neoplasms2CTD_human
TgeneC4704874Mammary Carcinoma, Human2CTD_human
TgeneC0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneC0002152Alloxan Diabetes1CTD_human
TgeneC0003493Aortic Diseases1CTD_human
TgeneC0003496Aortic Rupture1CTD_human
TgeneC0003873Rheumatoid Arthritis1CTD_human
TgeneC0005398Cholestasis, Extrahepatic1CTD_human
TgeneC0005684Malignant neoplasm of urinary bladder1CTD_human
TgeneC0005695Bladder Neoplasm1CTD_human
TgeneC0005940Bone Diseases1CTD_human
TgeneC0005944Metabolic Bone Disorder1CTD_human
TgeneC0005967Bone neoplasms1CTD_human
TgeneC0011853Diabetes Mellitus, Experimental1CTD_human
TgeneC0011882Diabetic Neuropathies1CTD_human
TgeneC0015934Fetal Growth Retardation1CTD_human
TgeneC0017636Glioblastoma1CTD_human
TgeneC0019193Hepatitis, Toxic1CTD_human
TgeneC0019207Hepatoma, Morris1CTD_human
TgeneC0019208Hepatoma, Novikoff1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0021368Inflammation1CTD_human
TgeneC0022682Kienbock Disease1CTD_human
TgeneC0023283Leishmaniasis, Cutaneous1CTD_human
TgeneC0023891Liver Cirrhosis, Alcoholic1CTD_human
TgeneC0023904Liver Neoplasms, Experimental1CTD_human
TgeneC0024143Lupus Nephritis1CTD_human
TgeneC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneC0024689Mandibular Diseases1CTD_human
TgeneC0024796Marfan Syndrome1CTD_human
TgeneC0024950Maxillary Diseases1CTD_human
TgeneC0027439Nasopharyngeal Neoplasms1CTD_human
TgeneC0027543Avascular necrosis of bone1CTD_human
TgeneC0028433Nose Neoplasms1CTD_human
TgeneC0029172Oral Submucous Fibrosis1CTD_human
TgeneC0029445Bone necrosis1CTD_human
TgeneC0029453Osteopenia1CTD_human
TgeneC0029463Osteosarcoma1CTD_human
TgeneC0030297Pancreatic Neoplasm1CTD_human
TgeneC0034067Pulmonary Emphysema1CTD_human
TgeneC0034069Pulmonary Fibrosis1CTD_human
TgeneC0038433Streptozotocin Diabetes1CTD_human
TgeneC0043094Weight Gain1CTD_human
TgeneC0085762Alcohol abuse1PSYGENET
TgeneC0086404Experimental Hepatoma1CTD_human
TgeneC0086540Leishmaniasis, New World1CTD_human
TgeneC0086541Urban cutaneous leishmaniasis1CTD_human
TgeneC0162872Aortic Aneurysm, Thoracic1CTD_human
TgeneC0221227Centriacinar Emphysema1CTD_human
TgeneC0235874Disease Exacerbation1CTD_human
TgeneC0238301Cancer of Nasopharynx1CTD_human
TgeneC0264393Panacinar Emphysema1CTD_human
TgeneC0271673Symmetric Diabetic Proximal Motor Neuropathy1CTD_human
TgeneC0271674Asymmetric Diabetic Proximal Motor Neuropathy1CTD_human
TgeneC0271678Diabetic Mononeuropathy1CTD_human
TgeneC0271680Diabetic Polyneuropathies1CTD_human
TgeneC0271685Diabetic Amyotrophy1CTD_human
TgeneC0271686Diabetic Autonomic Neuropathy1CTD_human
TgeneC0279530Malignant Bone Neoplasm1CTD_human
TgeneC0334588Giant Cell Glioblastoma1CTD_human
TgeneC0340630Aortic Aneurysm, Thoracoabdominal1CTD_human
TgeneC0346647Malignant neoplasm of pancreas1CTD_human
TgeneC0393835Diabetic Asymmetric Polyneuropathy1CTD_human
TgeneC0520474Aseptic Necrosis of Bone1CTD_human
TgeneC0741160Aortic Aneurysm, Ruptured1CTD_human
TgeneC0751074Diabetic Neuralgia1CTD_human
TgeneC0751394Cancer of Nose1CTD_human
TgeneC0860207Drug-Induced Liver Disease1CTD_human
TgeneC1262760Hepatitis, Drug-Induced1CTD_human
TgeneC1336708Testicular Germ Cell Tumor1CTD_human
TgeneC1621958Glioblastoma Multiforme1CTD_human
TgeneC2239176Liver carcinoma1CTD_human
TgeneC2350878Focal Emphysema1CTD_human
TgeneC2931822Nasopharyngeal carcinoma1CTD_human
TgeneC2936380Neointima1CTD_human
TgeneC2936381Neointima Formation1CTD_human
TgeneC2937358Cerebral Hemorrhage1CTD_human
TgeneC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneC4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneC4721507Alveolitis, Fibrosing1CTD_human
TgeneC4721845Marfan Syndrome, Type I1CTD_human