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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:TCF4-CSF2RA (FusionGDB2 ID:HG6925TG1438)

Fusion Gene Summary for TCF4-CSF2RA

check button Fusion gene summary
Fusion gene informationFusion gene name: TCF4-CSF2RA
Fusion gene ID: hg6925tg1438
HgeneTgene
Gene symbol

TCF4

CSF2RA

Gene ID

6925

1438

Gene nametranscription factor 4colony stimulating factor 2 receptor subunit alpha
SynonymsE2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19CD116|CDw116|CSF2R|CSF2RAX|CSF2RAY|CSF2RX|CSF2RY|GM-CSF-R-alpha|GMCSFR|GMCSFR-alpha|GMR|GMR-alpha|SMDP4|alphaGMR
Cytomap('TCF4')('CSF2RA')

18q21.2

Xp22.33 and Yp11.2

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor 4SL3-3 enhancer factor 2class B basic helix-loop-helix protein 19immunoglobulin transcription factor 2granulocyte-macrophage colony-stimulating factor receptor subunit alphaCD116 antigenGM-CSF receptor alpha subunitalpha-GM-CSF receptorcolony stimulating factor 2 receptor alpha subunitcolony stimulating factor 2 receptor, alpha, low-affinity (granulo
Modification date2020032920200326
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000354452, ENST00000356073, 
ENST00000398339, ENST00000457482, 
ENST00000537578, ENST00000537856, 
ENST00000540999, ENST00000543082, 
ENST00000544241, ENST00000561831, 
ENST00000561992, ENST00000563760, 
ENST00000564228, ENST00000564403, 
ENST00000564999, ENST00000565018, 
ENST00000566279, ENST00000566286, 
ENST00000567880, ENST00000568673, 
ENST00000568740, ENST00000570177, 
ENST00000570287, 
ENST00000354452, 
ENST00000356073, ENST00000398339, 
ENST00000457482, ENST00000537578, 
ENST00000537856, ENST00000540999, 
ENST00000543082, ENST00000544241, 
ENST00000561831, ENST00000561992, 
ENST00000563760, ENST00000564228, 
ENST00000564403, ENST00000564999, 
ENST00000565018, ENST00000566279, 
ENST00000566286, ENST00000567880, 
ENST00000568673, ENST00000568740, 
ENST00000570177, ENST00000570287, 
Fusion gene scores* DoF score13 X 13 X 4=6768 X 9 X 3=216
# samples 138
** MAII scorelog2(13/676*10)=-2.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/216*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TCF4 [Title/Abstract] AND CSF2RA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTCF4(53037568)-CSF2RA(1385211), # 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
HgeneTCF4

GO:0045893

positive regulation of transcription, DNA-templated

2105528|12651860



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 TCF4-CSF2RA

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 TCF4-CSF2RA


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 TCF4-CSF2RA


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/:53037568/:1385211)
- 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 TCF4-CSF2RA


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 TCF4-CSF2RA


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 TCF4-CSF2RA


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 TCF4-CSF2RA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTCF4C1970431PITT-HOPKINS SYNDROME14CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneTCF4C0005586Bipolar Disorder5PSYGENET
HgeneTCF4C0036341Schizophrenia4PSYGENET
HgeneTCF4C0016781Fuchs Endothelial Dystrophy1ORPHANET
HgeneTCF4C0018799Heart Diseases1CTD_human
HgeneTCF4C0022333Jacksonian Seizure1CTD_human
HgeneTCF4C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneTCF4C0023903Liver neoplasms1CTD_human
HgeneTCF4C0025958Microcephaly1CTD_human
HgeneTCF4C0033975Psychotic Disorders1PSYGENET
HgeneTCF4C0036572Seizures1CTD_human
HgeneTCF4C0149958Complex partial seizures1CTD_human
HgeneTCF4C0234533Generalized seizures1CTD_human
HgeneTCF4C0234535Clonic Seizures1CTD_human
HgeneTCF4C0270824Visual seizure1CTD_human
HgeneTCF4C0270844Tonic Seizures1CTD_human
HgeneTCF4C0270846Epileptic drop attack1CTD_human
HgeneTCF4C0345904Malignant neoplasm of liver1CTD_human
HgeneTCF4C0349204Nonorganic psychosis1PSYGENET
HgeneTCF4C0376634Craniofacial Abnormalities1CTD_human
HgeneTCF4C0422850Seizures, Somatosensory1CTD_human
HgeneTCF4C0422852Seizures, Auditory1CTD_human
HgeneTCF4C0422853Olfactory seizure1CTD_human
HgeneTCF4C0422854Gustatory seizure1CTD_human
HgeneTCF4C0422855Vertiginous seizure1CTD_human
HgeneTCF4C0494475Tonic - clonic seizures1CTD_human
HgeneTCF4C0566602Primary sclerosing cholangitis1ORPHANET
HgeneTCF4C0751056Non-epileptic convulsion1CTD_human
HgeneTCF4C0751110Single Seizure1CTD_human
HgeneTCF4C0751123Atonic Absence Seizures1CTD_human
HgeneTCF4C0751494Convulsive Seizures1CTD_human
HgeneTCF4C0751495Seizures, Focal1CTD_human
HgeneTCF4C0751496Seizures, Sensory1CTD_human
HgeneTCF4C1456784Paranoia1PSYGENET
HgeneTCF4C1535926Neurodevelopmental Disorders1CTD_human
HgeneTCF4C1956147Microlissencephaly1CTD_human
HgeneTCF4C2750451CORNEAL DYSTROPHY, FUCHS ENDOTHELIAL, 31CTD_human;GENOMICS_ENGLAND
HgeneTCF4C2931456Prostate cancer, familial1CTD_human
HgeneTCF4C3495874Nonepileptic Seizures1CTD_human
HgeneTCF4C3853041Severe Congenital Microcephaly1CTD_human
HgeneTCF4C4048158Convulsions1CTD_human
HgeneTCF4C4316903Absence Seizures1CTD_human
HgeneTCF4C4317109Epileptic Seizures1CTD_human
HgeneTCF4C4317123Myoclonic Seizures1CTD_human
HgeneTCF4C4505436Generalized Absence Seizures1CTD_human
HgeneTCF4C4721453Peripheral Nervous System Diseases1CTD_human
HgeneTCF4C4722327PROSTATE CANCER, HEREDITARY, 11CTD_human
TgeneC2677877Surfactant Metabolism Dysfunction, Pulmonary, 44CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0034050Pulmonary Alveolar Proteinosis3CTD_human;GENOMICS_ENGLAND
TgeneC0036341Schizophrenia2PSYGENET
TgeneC2931035Pulmonary alveolar proteinosis, congenital2GENOMICS_ENGLAND;ORPHANET
TgeneC0020517Hypersensitivity1GENOMICS_ENGLAND