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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:MED4-STAT5A (FusionGDB2 ID:HG29079TG6776)

Fusion Gene Summary for MED4-STAT5A

check button Fusion gene summary
Fusion gene informationFusion gene name: MED4-STAT5A
Fusion gene ID: hg29079tg6776
HgeneTgene
Gene symbol

MED4

STAT5A

Gene ID

29079

6776

Gene namemediator complex subunit 4signal transducer and activator of transcription 5A
SynonymsARC36|DRIP36|HSPC126|TRAP36|VDRIPMGF|STAT5
Cytomap('MED4')('STAT5A')

13q14.2

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionmediator of RNA polymerase II transcription subunit 4TRAP/SMCC/PC2 subunit p36activator-recruited cofactor 36 kDa componentmediator, 34-kD subunit, homologvitamin D receptor-interacting protein, 36-kDvitamin D3 receptor-interacting protein complex 36signal transducer and activator of transcription 5Aepididymis secretory sperm binding protein
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000258648, ENST00000378586, 
ENST00000495013, 
Fusion gene scores* DoF score6 X 6 X 4=1444 X 5 X 3=60
# samples 65
** MAII scorelog2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MED4 [Title/Abstract] AND STAT5A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMED4(48650838)-STAT5A(40458350), # samples:2
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
HgeneMED4

GO:0006366

transcription by RNA polymerase II

10882111

HgeneMED4

GO:0006367

transcription initiation from RNA polymerase II promoter

12218053

HgeneMED4

GO:0045893

positive regulation of transcription, DNA-templated

10198638

TgeneSTAT5A

GO:0038026

reelin-mediated signaling pathway

29581031



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 MED4-STAT5A

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 MED4-STAT5A


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 MED4-STAT5A


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/:48650838/:40458350)
- 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 MED4-STAT5A


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 MED4-STAT5A


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 MED4-STAT5A


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 MED4-STAT5A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMED4C0014175Endometriosis1CTD_human
HgeneMED4C0269102Endometrioma1CTD_human
TgeneC0024667Animal Mammary Neoplasms5CTD_human
TgeneC1257925Mammary Carcinoma, Animal5CTD_human
TgeneC0007097Carcinoma3CTD_human
TgeneC0024668Mammary Neoplasms, Experimental3CTD_human
TgeneC0205696Anaplastic carcinoma3CTD_human
TgeneC0205697Carcinoma, Spindle-Cell3CTD_human
TgeneC0205698Undifferentiated carcinoma3CTD_human
TgeneC0205699Carcinomatosis3CTD_human
TgeneC0001418Adenocarcinoma2CTD_human
TgeneC0205641Adenocarcinoma, Basal Cell2CTD_human
TgeneC0205642Adenocarcinoma, Oxyphilic2CTD_human
TgeneC0205643Carcinoma, Cribriform2CTD_human
TgeneC0205644Carcinoma, Granular Cell2CTD_human
TgeneC0205645Adenocarcinoma, Tubular2CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007124Noninfiltrating Intraductal Carcinoma1CTD_human
TgeneC0024121Lung Neoplasms1CTD_human
TgeneC0032927Precancerous Conditions1CTD_human
TgeneC0151744Myocardial Ischemia1CTD_human
TgeneC0206692Carcinoma, Lobular1CTD_human
TgeneC0242379Malignant neoplasm of lung1CTD_human
TgeneC0282313Condition, Preneoplastic1CTD_human
TgeneC0494261Combined immunodeficiency1GENOMICS_ENGLAND
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1176475Ductal Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1332347Atypical Ductal Breast Hyperplasia1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human