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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:TF-NEAT1 (FusionGDB2 ID:HG7018TG283131)

Fusion Gene Summary for TF-NEAT1

check button Fusion gene summary
Fusion gene informationFusion gene name: TF-NEAT1
Fusion gene ID: hg7018tg283131
HgeneTgene
Gene symbol

TF

NEAT1

Gene ID

7018

283131

Gene nametransferrinnuclear paraspeckle assembly transcript 1
SynonymsHEL-S-71p|PRO1557|PRO2086|TFQTL1LINC00084|NCRNA00084|TncRNA|VINC
Cytomap('TF')('NEAT1')

3q22.1

11q13.1

Type of geneprotein-codingncRNA
Descriptionserotransferrinbeta-1 metal-binding globulinepididymis secretory sperm binding protein Li 71psiderophilinMENepsilon/betalong intergenic non-protein coding RNA 84nuclear enriched abundant transcript 1nuclear paraspeckle assembly transcript 1 (non-protein coding)trophoblast MHC class II suppressortrophoblast-derived noncoding RNAvirus inducible non-codin
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000264998, ENST00000402696, 
ENST00000475382, 
Fusion gene scores* DoF score22 X 26 X 5=286024 X 31 X 2=1488
# samples 2831
** MAII scorelog2(28/2860*10)=-3.35251641472079
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(31/1488*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TF [Title/Abstract] AND NEAT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTF(133462520)-NEAT1(65191227), # 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
HgeneTF

GO:0048260

positive regulation of receptor-mediated endocytosis

12704209



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 TF-NEAT1

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 TF-NEAT1


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 TF-NEAT1


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/:133462520/:65191227)
- 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 TF-NEAT1


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 TF-NEAT1


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 TF-NEAT1


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 TF-NEAT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTFC0521802Congenital atransferrinemia5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneTFC0036341Schizophrenia3PSYGENET
HgeneTFC0001956Alcohol Use Disorder2CTD_human
HgeneTFC0001973Alcoholic Intoxication, Chronic2CTD_human
HgeneTFC0002395Alzheimer's Disease2CTD_human
HgeneTFC0007097Carcinoma2CTD_human
HgeneTFC0011265Presenile dementia2CTD_human
HgeneTFC0015695Fatty Liver2CTD_human
HgeneTFC0024667Animal Mammary Neoplasms2CTD_human
HgeneTFC0024668Mammary Neoplasms, Experimental2CTD_human
HgeneTFC0085762Alcohol abuse2CTD_human
HgeneTFC0205696Anaplastic carcinoma2CTD_human
HgeneTFC0205697Carcinoma, Spindle-Cell2CTD_human
HgeneTFC0205698Undifferentiated carcinoma2CTD_human
HgeneTFC0205699Carcinomatosis2CTD_human
HgeneTFC0276496Familial Alzheimer Disease (FAD)2CTD_human
HgeneTFC0494463Alzheimer Disease, Late Onset2CTD_human
HgeneTFC0546126Acute Confusional Senile Dementia2CTD_human
HgeneTFC0750900Alzheimer's Disease, Focal Onset2CTD_human
HgeneTFC0750901Alzheimer Disease, Early Onset2CTD_human
HgeneTFC1257925Mammary Carcinoma, Animal2CTD_human
HgeneTFC2711227Steatohepatitis2CTD_human
HgeneTFC0004352Autistic Disorder1CTD_human
HgeneTFC0013221Drug toxicity1CTD_human
HgeneTFC0013502Echinococcosis1CTD_human
HgeneTFC0019158Hepatitis1CTD_human
HgeneTFC0019193Hepatitis, Toxic1CTD_human
HgeneTFC0021368Inflammation1CTD_human
HgeneTFC0022660Kidney Failure, Acute1CTD_human
HgeneTFC0027626Neoplasm Invasiveness1CTD_human
HgeneTFC0027726Nephrotic Syndrome1CTD_human
HgeneTFC0028754Obesity1CTD_human
HgeneTFC0030524Paratuberculosis1CTD_human
HgeneTFC0035258Restless Legs Syndrome1CTD_human
HgeneTFC0041755Adverse reaction to drug1CTD_human
HgeneTFC0152013Adenocarcinoma of lung (disorder)1CTD_human
HgeneTFC0271901Microcytic hypochromic anemia (disorder)1CTD_human
HgeneTFC0282193Iron Overload1CTD_human
HgeneTFC0345967Malignant mesothelioma1CTD_human
HgeneTFC0860207Drug-Induced Liver Disease1CTD_human
HgeneTFC1262760Hepatitis, Drug-Induced1CTD_human
HgeneTFC1565662Acute Kidney Insufficiency1CTD_human
HgeneTFC2609414Acute kidney injury1CTD_human
HgeneTFC3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneTFC4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneTFC4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneTFC4553297Cystic Echinocccosis1CTD_human
TgeneC0023903Liver neoplasms1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0087031Juvenile-Onset Still Disease1CTD_human
TgeneC0345904Malignant neoplasm of liver1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC3495559Juvenile arthritis1CTD_human
TgeneC3714758Juvenile psoriatic arthritis1CTD_human
TgeneC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
TgeneC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human