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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:GATA3-NBEA (FusionGDB2 ID:HG2625TG26960)

Fusion Gene Summary for GATA3-NBEA

check button Fusion gene summary
Fusion gene informationFusion gene name: GATA3-NBEA
Fusion gene ID: hg2625tg26960
HgeneTgene
Gene symbol

GATA3

NBEA

Gene ID

2625

26960

Gene nameGATA binding protein 3neurobeachin
SynonymsHDR|HDRSBCL8B|LYST2
Cytomap('GATA3')('NBEA')

10p14

13q13.3

Type of geneprotein-codingprotein-coding
Descriptiontrans-acting T-cell-specific transcription factor GATA-3GATA-binding factor 3neurobeachinlysosomal-trafficking regulator 2
Modification date2020032220200328
UniProtAcc

P23771

.
Ensembl transtripts involved in fusion geneENST00000379328, ENST00000346208, 
ENST00000461472, 
Fusion gene scores* DoF score4 X 5 X 2=4017 X 16 X 6=1632
# samples 518
** MAII scorelog2(5/40*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(18/1632*10)=-3.18057224564182
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GATA3 [Title/Abstract] AND NBEA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGATA3(8116847)-NBEA(35673355), # 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
HgeneGATA3

GO:0033600

negative regulation of mammary gland epithelial cell proliferation

19483726

HgeneGATA3

GO:0045893

positive regulation of transcription, DNA-templated

19723756|19805038

HgeneGATA3

GO:0045944

positive regulation of transcription by RNA polymerase II

19232384|20189993|20484083

HgeneGATA3

GO:0060231

mesenchymal to epithelial transition

20189993

HgeneGATA3

GO:0072676

lymphocyte migration

19805038

HgeneGATA3

GO:2000664

positive regulation of interleukin-5 secretion

20554961

HgeneGATA3

GO:2000667

positive regulation of interleukin-13 secretion

20554961



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 GATA3-NBEA

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 GATA3-NBEA


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 GATA3-NBEA


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/:8116847/:35673355)
- 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
GATA3

P23771

.
FUNCTION: Transcriptional activator which binds to the enhancer of the T-cell receptor alpha and delta genes. Binds to the consensus sequence 5'-AGATAG-3'. Required for the T-helper 2 (Th2) differentiation process following immune and inflammatory responses. {ECO:0000269|PubMed:23824597}.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 GATA3-NBEA


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 GATA3-NBEA


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 GATA3-NBEA


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 GATA3-NBEA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGATA3C1840333Barakat syndrome16CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneGATA3C0006413Burkitt Lymphoma3ORPHANET
HgeneGATA3C1292769Precursor B-cell lymphoblastic leukemia3ORPHANET
HgeneGATA3C0003873Rheumatoid Arthritis1CTD_human
HgeneGATA3C0007097Carcinoma1CTD_human
HgeneGATA3C0014457Eosinophilia1CTD_human
HgeneGATA3C0014458Eosinophilia, Tropical1CTD_human
HgeneGATA3C0019829Hodgkin Disease1CTD_human
HgeneGATA3C0021368Inflammation1CTD_human
HgeneGATA3C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma1CTD_human
HgeneGATA3C0023493Adult T-Cell Lymphoma/Leukemia1CTD_human
HgeneGATA3C0024667Animal Mammary Neoplasms1CTD_human
HgeneGATA3C0024668Mammary Neoplasms, Experimental1CTD_human
HgeneGATA3C0025568Metaplasia1CTD_human
HgeneGATA3C0027819Neuroblastoma1CTD_human
HgeneGATA3C0152266Mixed Cellularity Hodgkin Lymphoma1CTD_human
HgeneGATA3C0152267Hodgkin lymphoma, lymphocyte depletion1CTD_human
HgeneGATA3C0205696Anaplastic carcinoma1CTD_human
HgeneGATA3C0205697Carcinoma, Spindle-Cell1CTD_human
HgeneGATA3C0205698Undifferentiated carcinoma1CTD_human
HgeneGATA3C0205699Carcinomatosis1CTD_human
HgeneGATA3C0220597Adult Hodgkin Lymphoma1CTD_human
HgeneGATA3C1257925Mammary Carcinoma, Animal1CTD_human
HgeneGATA3C1266194Lymphocyte Rich Classical Hodgkin Lymphoma1CTD_human
HgeneGATA3C1334968Nodular Lymphocyte Predominant Hodgkin Lymphoma1CTD_human
HgeneGATA3C2930967Gastro-enteropancreatic neuroendocrine tumor1CTD_human
TgeneC0004352Autistic Disorder2CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0036572Seizures1GENOMICS_ENGLAND
TgeneC0557874Global developmental delay1GENOMICS_ENGLAND
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND