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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:SMARCA4-FOXO1 (FusionGDB2 ID:83891)

Fusion Gene Summary for SMARCA4-FOXO1

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCA4-FOXO1
Fusion gene ID: 83891
HgeneTgene
Gene symbol

SMARCA4

FOXO1

Gene ID

6597

2308

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4forkhead box O1
SynonymsBAF190|BAF190A|BRG1|CSS4|MRD16|RTPS2|SNF2|SNF2-beta|SNF2L4|SNF2LB|SWI2|hSNF2bFKH1|FKHR|FOXO1A
Cytomap

19p13.2

13q14.11

Type of geneprotein-codingprotein-coding
Descriptiontranscription activator BRG1ATP-dependent helicase SMARCA4BRG1-associated factor 190ABRM/SWI2-related gene 1SNF2-like 4brahma protein-like 1global transcription activator homologous sequencehomeotic gene regulatormitotic growth and transcription aforkhead box protein O1forkhead box protein O1Aforkhead, Drosophila, homolog of, in rhabdomyosarcoma
Modification date2020031520200322
UniProtAcc.

Q12778

Ensembl transtripts involved in fusion geneENST00000344626, ENST00000358026, 
ENST00000413806, ENST00000429416, 
ENST00000444061, ENST00000450717, 
ENST00000538456, ENST00000541122, 
ENST00000589677, ENST00000590574, 
ENST00000379561, ENST00000473775, 
Fusion gene scores* DoF score29 X 29 X 17=1429711 X 11 X 7=847
# samples 5514
** MAII scorelog2(55/14297*10)=-4.70013702309346
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(14/847*10)=-2.59693514238723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMARCA4 [Title/Abstract] AND FOXO1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMARCA4(11152236)-FOXO1(41048232), # 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
HgeneSMARCA4

GO:0006337

nucleosome disassembly

8895581

HgeneSMARCA4

GO:0006338

chromatin remodeling

10943845|11726552

HgeneSMARCA4

GO:0045892

negative regulation of transcription, DNA-templated

12065415

HgeneSMARCA4

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904|17938176

HgeneSMARCA4

GO:0051091

positive regulation of DNA-binding transcription factor activity

11950834|17938176

HgeneSMARCA4

GO:1902661

positive regulation of glucose mediated signaling pathway

22368283

TgeneFOXO1

GO:0009267

cellular response to starvation

20543840

TgeneFOXO1

GO:0032873

negative regulation of stress-activated MAPK cascade

19696738

TgeneFOXO1

GO:0043066

negative regulation of apoptotic process

10871843

TgeneFOXO1

GO:0045893

positive regulation of transcription, DNA-templated

7862145|10871843|12228231

TgeneFOXO1

GO:0045944

positive regulation of transcription by RNA polymerase II

10871843|12228231

TgeneFOXO1

GO:0071455

cellular response to hyperoxia

20543840


check buttonFusion gene breakpoints across SMARCA4 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across FOXO1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4LUADTCGA-50-6591-01ASMARCA4chr19

11152236

+FOXO1chr13

41048232

-


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Fusion Gene ORF analysis for SMARCA4-FOXO1

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
5CDS-intronENST00000344626ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000344626ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000358026ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000358026ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000413806ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000413806ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000429416ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000429416ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000444061ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000444061ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000450717ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000450717ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000538456ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000538456ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000541122ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000541122ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000589677ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000589677ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000590574ENST00000379561SMARCA4chr19

11152236

+FOXO1chr13

41048232

-
5CDS-intronENST00000590574ENST00000473775SMARCA4chr19

11152236

+FOXO1chr13

41048232

-

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 SMARCA4-FOXO1


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for SMARCA4-FOXO1


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/:11152236/:41048232)
- 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
.FOXO1

Q12778

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: Transcription factor that is the main target of insulin signaling and regulates metabolic homeostasis in response to oxidative stress (PubMed:10358076, PubMed:12228231, PubMed:15220471, PubMed:15890677, PubMed:18356527, PubMed:19221179, PubMed:20543840, PubMed:21245099). Binds to the insulin response element (IRE) with consensus sequence 5'-TT[G/A]TTTTG-3' and the related Daf-16 family binding element (DBE) with consensus sequence 5'-TT[G/A]TTTAC-3' (PubMed:10358076). Activity suppressed by insulin (PubMed:10358076). Main regulator of redox balance and osteoblast numbers and controls bone mass (By similarity). Orchestrates the endocrine function of the skeleton in regulating glucose metabolism (By similarity). Also acts as a key regulator of chondrogenic commitment of skeletal progenitor cells in response to lipid availability: when lipids levels are low, translocates to the nucleus and promotes expression of SOX9, which induces chondrogenic commitment and suppresses fatty acid oxidation (By similarity). Acts synergistically with ATF4 to suppress osteocalcin/BGLAP activity, increasing glucose levels and triggering glucose intolerance and insulin insensitivity (By similarity). Also suppresses the transcriptional activity of RUNX2, an upstream activator of osteocalcin/BGLAP (By similarity). In hepatocytes, promotes gluconeogenesis by acting together with PPARGC1A and CEBPA to activate the expression of genes such as IGFBP1, G6PC1 and PCK1 (By similarity). Important regulator of cell death acting downstream of CDK1, PKB/AKT1 and STK4/MST1 (PubMed:18356527, PubMed:19221179). Promotes neural cell death (PubMed:18356527). Mediates insulin action on adipose tissue (By similarity). Regulates the expression of adipogenic genes such as PPARG during preadipocyte differentiation and, adipocyte size and adipose tissue-specific gene expression in response to excessive calorie intake (By similarity). Regulates the transcriptional activity of GADD45A and repair of nitric oxide-damaged DNA in beta-cells (By similarity). Required for the autophagic cell death induction in response to starvation or oxidative stress in a transcription-independent manner (PubMed:20543840). Mediates the function of MLIP in cardiomyocytes hypertrophy and cardiac remodeling (By similarity). Regulates endothelial cell (EC) viability and apoptosis in a PPIA/CYPA-dependent manner via transcription of CCL2 and BCL2L11 which are involved in EC chemotaxis and apoptosis (PubMed:31063815). {ECO:0000250|UniProtKB:A4L7N3, ECO:0000250|UniProtKB:G3V7R4, ECO:0000250|UniProtKB:Q9R1E0, ECO:0000269|PubMed:10358076, ECO:0000269|PubMed:12228231, ECO:0000269|PubMed:15220471, ECO:0000269|PubMed:15890677, ECO:0000269|PubMed:18356527, ECO:0000269|PubMed:19221179, ECO:0000269|PubMed:20543840, ECO:0000269|PubMed:21245099, ECO:0000269|PubMed:31063815}.

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 SMARCA4-FOXO1


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 SMARCA4-FOXO1


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 SMARCA4-FOXO1


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 SMARCA4-FOXO1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource