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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:TFPI-ARID1A (FusionGDB2 ID:HG7035TG8289)

Fusion Gene Summary for TFPI-ARID1A

check button Fusion gene summary
Fusion gene informationFusion gene name: TFPI-ARID1A
Fusion gene ID: hg7035tg8289
HgeneTgene
Gene symbol

TFPI

ARID1A

Gene ID

7035

8289

Gene nametissue factor pathway inhibitorAT-rich interaction domain 1A
SynonymsEPI|LACI|TFI|TFPI1B120|BAF250|BAF250a|BM029|C1orf4|CSS2|ELD|MRD14|OSA1|P270|SMARCF1|hELD|hOSA1
Cytomap('TFPI')('ARID1A')

2q32.1

1p36.11

Type of geneprotein-codingprotein-coding
Descriptiontissue factor pathway inhibitoranti-convertinextrinsic pathway inhibitortissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)AT-rich interactive domain-containing protein 1AARID domain-containing protein 1AAT rich interactive domain 1A (SWI-like)BRG1-associated factor 250aOSA1 nuclear proteinSWI-like proteinSWI/SNF complex protein p270SWI/SNF-related, matrix-associated,
Modification date2020031320200329
UniProtAcc.

O14497

Ensembl transtripts involved in fusion geneENST00000233156, ENST00000339091, 
ENST00000392365, ENST00000409676, 
Fusion gene scores* DoF score4 X 3 X 3=3613 X 16 X 6=1248
# samples 417
** MAII scorelog2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(17/1248*10)=-2.87601128272455
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TFPI [Title/Abstract] AND ARID1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTFPI(188369030)-ARID1A(27108477), # 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
HgeneTFPI

GO:0030195

negative regulation of blood coagulation

21868574

TgeneARID1A

GO:0006337

nucleosome disassembly

8895581

TgeneARID1A

GO:0006338

chromatin remodeling

11726552

TgeneARID1A

GO:0030520

intracellular estrogen receptor signaling pathway

12200431

TgeneARID1A

GO:0030521

androgen receptor signaling pathway

12200431

TgeneARID1A

GO:0042921

glucocorticoid receptor signaling pathway

12200431

TgeneARID1A

GO:0045893

positive regulation of transcription, DNA-templated

12200431



check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChiTaRS5.0N/ABQ187382TFPIchr2

188369030

-ARID1Achr1

27108477

+


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Fusion Gene ORF analysis for TFPI-ARID1A

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
intron-3UTRENST00000233156ENST00000324856TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-3UTRENST00000339091ENST00000324856TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-3UTRENST00000392365ENST00000324856TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-3UTRENST00000409676ENST00000324856TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000233156ENST00000374152TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000233156ENST00000457599TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000233156ENST00000540690TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000339091ENST00000374152TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000339091ENST00000457599TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000339091ENST00000540690TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000392365ENST00000374152TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000392365ENST00000457599TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000392365ENST00000540690TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000409676ENST00000374152TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000409676ENST00000457599TFPIchr2

188369030

-ARID1Achr1

27108477

+
intron-intronENST00000409676ENST00000540690TFPIchr2

188369030

-ARID1Achr1

27108477

+

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 TFPI-ARID1A


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 TFPI-ARID1A


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/:188369030/:27108477)
- 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
.ARID1A

O14497

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: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. Binds DNA non-specifically. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). {ECO:0000250|UniProtKB:A2BH40, ECO:0000303|PubMed:12672490, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.

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 TFPI-ARID1A


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 TFPI-ARID1A


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 TFPI-ARID1A


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 TFPI-ARID1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTFPIC0001883Airway Obstruction1CTD_human
HgeneTFPIC0003129Anoxemia1CTD_human
HgeneTFPIC0003130Anoxia1CTD_human
HgeneTFPIC0008301Choking1CTD_human
HgeneTFPIC0034155Purpura, Thrombotic Thrombocytopenic1CTD_human
HgeneTFPIC0042487Venous Thrombosis1CTD_human
HgeneTFPIC0087031Juvenile-Onset Still Disease1CTD_human
HgeneTFPIC0149871Deep Vein Thrombosis1CTD_human
HgeneTFPIC0242184Hypoxia1CTD_human
HgeneTFPIC0600433Activated Protein C Resistance1CTD_human
HgeneTFPIC0700292Hypoxemia1CTD_human
HgeneTFPIC1268935Congenital Thrombotic Thrombocytopenic Purpura1CTD_human
HgeneTFPIC1956258Familial Thrombotic Thrombocytopenic Purpura1CTD_human
HgeneTFPIC3495559Juvenile arthritis1CTD_human
HgeneTFPIC3714758Juvenile psoriatic arthritis1CTD_human
HgeneTFPIC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneTFPIC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneC0024623Malignant neoplasm of stomach3CTD_human
TgeneC0038356Stomach Neoplasms3CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer3CTD_human
TgeneC2239176Liver carcinoma3CTD_human
TgeneC0033578Prostatic Neoplasms2CTD_human
TgeneC0376358Malignant neoplasm of prostate2CTD_human
TgeneC0001418Adenocarcinoma1CTD_human
TgeneC0005684Malignant neoplasm of urinary bladder1CTD_human
TgeneC0005695Bladder Neoplasm1CTD_human
TgeneC0006413Burkitt Lymphoma1CTD_human
TgeneC0007138Carcinoma, Transitional Cell1CTD_human
TgeneC0009402Colorectal Carcinoma1CTD_human
TgeneC0009404Colorectal Neoplasms1CTD_human
TgeneC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneC0014170Endometrial Neoplasms1CTD_human
TgeneC0027708Nephroblastoma1CTD_human
TgeneC0027819Neuroblastoma1CTD_human
TgeneC0036920Sezary Syndrome1CTD_human
TgeneC0079772T-Cell Lymphoma1CTD_human
TgeneC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
TgeneC0205641Adenocarcinoma, Basal Cell1CTD_human
TgeneC0205642Adenocarcinoma, Oxyphilic1CTD_human
TgeneC0205643Carcinoma, Cribriform1CTD_human
TgeneC0205644Carcinoma, Granular Cell1CTD_human
TgeneC0205645Adenocarcinoma, Tubular1CTD_human
TgeneC0206656Embryonal Rhabdomyosarcoma1CTD_human
TgeneC0206698Cholangiocarcinoma1CTD_human
TgeneC0265338Coffin-Siris syndrome1CTD_human;GENOMICS_ENGLAND
TgeneC0279628Adenocarcinoma Of Esophagus1CTD_human
TgeneC0343640African Burkitt's lymphoma1CTD_human
TgeneC0345905Intrahepatic Cholangiocarcinoma1CTD_human
TgeneC0376407Granulomatous Slack Skin1CTD_human
TgeneC0476089Endometrial Carcinoma1CTD_human
TgeneC0920269Microsatellite Instability1CTD_human
TgeneC1721098Replication Error Phenotype1CTD_human
TgeneC2930471Bilateral Wilms Tumor1CTD_human
TgeneC2931822Nasopharyngeal carcinoma1CTD_human
TgeneC3805278Extrahepatic Cholangiocarcinoma1CTD_human
TgeneC4721444Burkitt Leukemia1CTD_human