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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:FOXO1-UBQLN1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FOXO1-UBQLN1
	FusionPDB ID: 31171
	FusionGDB2.0 ID: 31171
		Hgene	Tgene
	Gene symbol	FOXO1	UBQLN1
	Gene ID	2308	29979
	Gene name	forkhead box O1	ubiquilin 1
	Synonyms	FKH1\|FKHR\|FOXO1A	DA41\|DSK2\|PLIC-1\|UBQN\|XDRP1
	Cytomap	13q14.11	9q21.32\|9q21.2-q21.3
	Type of gene	protein-coding	protein-coding
	Description	forkhead box protein O1forkhead box protein O1Aforkhead, Drosophila, homolog of, in rhabdomyosarcoma	ubiquilin-1hPLIC-1protein linking IAP with cytoskeleton 1testicular tissue protein Li 219
	Modification date	20200322	20200327
	UniProtAcc	Q12778	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000379561, ENST00000473775,	ENST00000257468, ENST00000376395,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 12 X 9=1404	15 X 10 X 9=1350
	# samples	16	19
	** MAII score	log2(16/1404*10)=-3.1333991254172 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(19/1350*10)=-2.82888808360725 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: FOXO1 [Title/Abstract] AND UBQLN1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FOXO1(41239719)-UBQLN1(86280060), # samples:1
Anticipated loss of major functional domain due to fusion event.	FOXO1-UBQLN1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. FOXO1-UBQLN1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. FOXO1-UBQLN1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. FOXO1-UBQLN1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	FOXO1	GO:0009267	cellular response to starvation	20543840
Hgene	FOXO1	GO:0032873	negative regulation of stress-activated MAPK cascade	19696738
Hgene	FOXO1	GO:0043066	negative regulation of apoptotic process	10871843
Hgene	FOXO1	GO:0045893	positive regulation of transcription, DNA-templated	7862145\|10871843\|12228231
Hgene	FOXO1	GO:0045944	positive regulation of transcription by RNA polymerase II	10871843\|12228231
Hgene	FOXO1	GO:0071455	cellular response to hyperoxia	20543840
Tgene	UBQLN1	GO:0031396	regulation of protein ubiquitination	12634373
Tgene	UBQLN1	GO:0031398	positive regulation of protein ubiquitination	23307288
Tgene	UBQLN1	GO:0035973	aggrephagy	21143716

Fusion gene breakpoints across FOXO1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across UBQLN1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	STAD	TCGA-BR-A453	FOXO1	chr13	41239719	-	UBQLN1	chr9	86280060	-

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000379561	FOXO1	chr13	41239719	-	ENST00000376395	UBQLN1	chr9	86280060	-	3277	1015	43	1452	469
ENST00000379561	FOXO1	chr13	41239719	-	ENST00000257468	UBQLN1	chr9	86280060	-	1811	1015	43	1452	469

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000379561	ENST00000376395	FOXO1	chr13	41239719	-	UBQLN1	chr9	86280060	-	0.002854042	0.99714595
ENST00000379561	ENST00000257468	FOXO1	chr13	41239719	-	UBQLN1	chr9	86280060	-	0.03317468	0.96682537

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>31171_31171_1_FOXO1-UBQLN1_FOXO1_chr13_41239719_ENST00000379561_UBQLN1_chr9_86280060_ENST00000257468_length(amino acids)=469AA_BP=324
MGRASGPRRPSVLPSAALSAGARRRLCPGPAALAGRPVRAADPEEPRCGWPREVKFWARASTPPRLPPSFRPLAAPASFPQISDRPFAPP
PRPPPVLRSPPLGSPAAGGGAGVTMAEAPQVVEIDPDFEPLPRPRSCTWPLPRPEFSQSNSATSSPAPSGSAAANPDAAAGLPSASAAAV
SADFMSNLSLLEESEDFPQAPGSVAAAVAAAAAAAATGGLCGDFQGPEAGCLHPAPPQPPPPGPLSQHPPVPPAAAGPLAGQPRKSSSSR
RNAWGNLSYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGL
IPGFTPGLGALGSTGGSSGTNGSNATPSENTSPTAGTTEPGHQQFIQQMLQALAGVNPQLQNPEVRFQQQLEQLSAMGFLNREANLQALI

--------------------------------------------------------------

>31171_31171_2_FOXO1-UBQLN1_FOXO1_chr13_41239719_ENST00000379561_UBQLN1_chr9_86280060_ENST00000376395_length(amino acids)=469AA_BP=324
MGRASGPRRPSVLPSAALSAGARRRLCPGPAALAGRPVRAADPEEPRCGWPREVKFWARASTPPRLPPSFRPLAAPASFPQISDRPFAPP
PRPPPVLRSPPLGSPAAGGGAGVTMAEAPQVVEIDPDFEPLPRPRSCTWPLPRPEFSQSNSATSSPAPSGSAAANPDAAAGLPSASAAAV
SADFMSNLSLLEESEDFPQAPGSVAAAVAAAAAAAATGGLCGDFQGPEAGCLHPAPPQPPPPGPLSQHPPVPPAAAGPLAGQPRKSSSSR
RNAWGNLSYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGL
IPGFTPGLGALGSTGGSSGTNGSNATPSENTSPTAGTTEPGHQQFIQQMLQALAGVNPQLQNPEVRFQQQLEQLSAMGFLNREANLQALI

--------------------------------------------------------------

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr13:41239719/chr9:86280060)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
FOXO1 Q12778	.
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}.	FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

Retention 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.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

FOXO1

chr13:41239719

chr9:86280060

ENST00000379561

120_130

210.0

1440.3333333333333

Compositional bias

Note=Poly-Pro

Hgene

FOXO1

chr13:41239719

chr9:86280060

ENST00000379561

152_155

210.0

1440.3333333333333

Compositional bias

Note=Poly-Ser

Hgene

FOXO1

chr13:41239719

chr9:86280060

ENST00000379561

91_102

210.0

1440.3333333333333

Compositional bias

Note=Poly-Ala

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000257468

438_470

416.0

562.0

Domain

STI1 4

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000257468

546_586

416.0

562.0

Domain

UBA

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000376395

546_586

444.0

590.0

Domain

UBA

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

FOXO1

chr13:41239719

chr9:86280060

ENST00000379561

159_235

210.0

1440.3333333333333

DNA binding

Fork-head

Hgene

FOXO1

chr13:41239719

chr9:86280060

ENST00000379561

211_218

210.0

1440.3333333333333

Region

Note=DNA-binding

Hgene

FOXO1

chr13:41239719

chr9:86280060

ENST00000379561

234_237

210.0

1440.3333333333333

Region

Note=DNA-binding

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000257468

182_210

416.0

562.0

Domain

STI1 1

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000257468

212_251

416.0

562.0

Domain

STI1 2

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000257468

37_111

416.0

562.0

Domain

Ubiquitin-like

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000257468

387_434

416.0

562.0

Domain

STI1 3

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000376395

182_210

444.0

590.0

Domain

STI1 1

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000376395

212_251

444.0

590.0

Domain

STI1 2

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000376395

37_111

444.0

590.0

Domain

Ubiquitin-like

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000376395

387_434

444.0

590.0

Domain

STI1 3

Tgene

UBQLN1

chr13:41239719

chr9:86280060

ENST00000376395

438_470

444.0

590.0

Domain

STI1 4

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
FOXO1
UBQLN1

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Tgene	UBQLN1	chr13:41239719	chr9:86280060	ENST00000257468		6	10	178_428	416.0	562.0	UBXN4
Tgene	UBQLN1	chr13:41239719	chr9:86280060	ENST00000376395		7	11	178_428	444.0	590.0	UBXN4

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Related Drugs to FOXO1-UBQLN1

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to FOXO1-UBQLN1

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	FOXO1	C0020542	Pulmonary Hypertension	1	CTD_human
Hgene	FOXO1	C0022578	Keratoconus	1	CTD_human
Hgene	FOXO1	C0023467	Leukemia, Myelocytic, Acute	1	CTD_human
Hgene	FOXO1	C0026998	Acute Myeloid Leukemia, M1	1	CTD_human
Hgene	FOXO1	C0033578	Prostatic Neoplasms	1	CTD_human
Hgene	FOXO1	C0206655	Alveolar rhabdomyosarcoma	1	CTD_human;GENOMICS_ENGLAND;ORPHANET
Hgene	FOXO1	C0376358	Malignant neoplasm of prostate	1	CTD_human
Hgene	FOXO1	C1879321	Acute Myeloid Leukemia (AML-M2)	1	CTD_human