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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:MDK-TMED2 (FusionGDB2 ID:HG4192TG10959)

Fusion Gene Summary for MDK-TMED2

check button Fusion gene summary
Fusion gene informationFusion gene name: MDK-TMED2
Fusion gene ID: hg4192tg10959
HgeneTgene
Gene symbol

MDK

TMED2

Gene ID

4192

10959

Gene namemidkinetransmembrane p24 trafficking protein 2
SynonymsARAP|MK|NEGF2P24A|RNP24|p24|p24b1|p24beta1
Cytomap('MDK')('TMED2')

11p11.2

12q24.31

Type of geneprotein-codingprotein-coding
Descriptionmidkineamphiregulin-associated proteinmidgestation and kidney proteinneurite growth-promoting factor 2neurite outgrowth-promoting factor 2retinoic acid inducible factortransmembrane emp24 domain-containing protein 2coated vesicle membrane proteinmembrane protein p24Ap24 family protein beta-1transmembrane emp24 domain trafficking protein 2
Modification date2020031520200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000359803, ENST00000395565, 
ENST00000395566, ENST00000395569, 
ENST00000405308, ENST00000407067, 
ENST00000533283, 
Fusion gene scores* DoF score7 X 5 X 5=1756 X 8 X 3=144
# samples 78
** MAII scorelog2(7/175*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/144*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MDK [Title/Abstract] AND TMED2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMDK(46405298)-TMED2(124081861), # 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
HgeneMDK

GO:0010838

positive regulation of keratinocyte proliferation

18469519

HgeneMDK

GO:0010976

positive regulation of neuron projection development

12084985

HgeneMDK

GO:0030335

positive regulation of cell migration

15466886

HgeneMDK

GO:0043524

negative regulation of neuron apoptotic process

12573468

HgeneMDK

GO:0045785

positive regulation of cell adhesion

12084985

HgeneMDK

GO:0048714

positive regulation of oligodendrocyte differentiation

27445335

HgeneMDK

GO:2000249

regulation of actin cytoskeleton reorganization

18469519

TgeneTMED2

GO:0006886

intracellular protein transport

20427317

TgeneTMED2

GO:0034260

negative regulation of GTPase activity

10761932

TgeneTMED2

GO:0072659

protein localization to plasma membrane

20361938



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


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Fusion Gene ORF analysis for MDK-TMED2

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

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 MDK-TMED2


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)


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Fusion Protein Features for MDK-TMED2


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/:46405298/:124081861)
- 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 MDK-TMED2


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 MDK-TMED2


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 MDK-TMED2


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 MDK-TMED2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMDKC0003469Anxiety Disorders1CTD_human
HgeneMDKC0011881Diabetic Nephropathy1CTD_human
HgeneMDKC0017638Glioma1CTD_human
HgeneMDKC0017667Nodular glomerulosclerosis1CTD_human
HgeneMDKC0025261Memory Disorders1CTD_human
HgeneMDKC0036341Schizophrenia1PSYGENET
HgeneMDKC0233794Memory impairment1CTD_human
HgeneMDKC0259783mixed gliomas1CTD_human
HgeneMDKC0345967Malignant mesothelioma1CTD_human
HgeneMDKC0376280Anxiety States, Neurotic1CTD_human
HgeneMDKC0555198Malignant Glioma1CTD_human
HgeneMDKC0751292Age-Related Memory Disorders1CTD_human
HgeneMDKC0751293Memory Disorder, Semantic1CTD_human
HgeneMDKC0751294Memory Disorder, Spatial1CTD_human
HgeneMDKC0751295Memory Loss1CTD_human
HgeneMDKC1279420Anxiety neurosis (finding)1CTD_human
TgeneC0151744Myocardial Ischemia1CTD_human