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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:NFE2L1-NPEPPS (FusionGDB2 ID:58825)

Fusion Gene Summary for NFE2L1-NPEPPS

Fusion gene summary

Fusion gene information	Fusion gene name: NFE2L1-NPEPPS
	Fusion gene ID: 58825
		Hgene	Tgene
	Gene symbol	NFE2L1	NPEPPS
	Gene ID	4779	9520
	Gene name	nuclear factor, erythroid 2 like 1	aminopeptidase puromycin sensitive
	Synonyms	LCR-F1\|NRF1\|TCF11	AAP-S\|MP100\|PSA
	Cytomap	17q21.32	17q21.32
	Type of gene	protein-coding	protein-coding
	Description	endoplasmic reticulum membrane sensor NFE2L1NF-E2-related factor 1NFE2-related factor 1TCF-11locus control region-factor 1nuclear factor erythroid 2-related factor 1nuclear factor, erythroid derived 2, like 1protein NRF1, p120 formtranscription fa	puromycin-sensitive aminopeptidasecytosol alanyl aminopeptidasemetalloproteinase MP100
	Modification date	20200313	20200313
	UniProtAcc	Q14494	P55786
	Ensembl transtripts involved in fusion gene	ENST00000357480, ENST00000362042, ENST00000585291, ENST00000361665, ENST00000536222, ENST00000579481, ENST00000582155, ENST00000583378,	ENST00000322157, ENST00000525037, ENST00000530173, ENST00000544660,
Fusion gene scores	* DoF score	18 X 12 X 13=2808	14 X 15 X 9=1890
	# samples	20	17
	** MAII score	log2(20/2808*10)=-3.81147103052984 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(17/1890*10)=-3.47477958297073 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: NFE2L1 [Title/Abstract] AND NPEPPS [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	NFE2L1(46125824)-NPEPPS(45673719), # samples:3
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)

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
Tgene	NPEPPS	GO:0071456	cellular response to hypoxia	21056661

Fusion gene breakpoints across NFE2L1 (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 NPEPPS (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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	ACC	TCGA-OR-A5J7-01A	NFE2L1	chr17	46125824	-	NPEPPS	chr17	45673719	+
ChimerDB4	ACC	TCGA-OR-A5J7-01A	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
ChimerDB4	ACC	TCGA-OR-A5J7	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+

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Fusion Gene ORF analysis for NFE2L1-NPEPPS

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5UTR-intron	ENST00000357480	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000357480	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000357480	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000357480	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000357480	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000357480	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000357480	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000357480	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000362042	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000362042	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000362042	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000362042	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000362042	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000362042	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000362042	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000362042	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000585291	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000585291	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000585291	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000585291	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000585291	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000585291	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
5UTR-intron	ENST00000585291	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
5UTR-intron	ENST00000585291	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000361665	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000361665	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000361665	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000361665	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000361665	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000361665	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000361665	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000361665	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000536222	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000536222	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000536222	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000536222	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000536222	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000536222	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000536222	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000536222	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000579481	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000579481	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000579481	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000579481	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000579481	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000579481	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000579481	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000579481	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000582155	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000582155	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000582155	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000582155	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000582155	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000582155	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000582155	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000582155	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000583378	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000583378	ENST00000322157	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000583378	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000583378	ENST00000525037	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000583378	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000583378	ENST00000530173	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+
intron-intron	ENST00000583378	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673719	+
intron-intron	ENST00000583378	ENST00000544660	NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

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

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Fusion Genomic Features for NFE2L1-NPEPPS

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+	5.32E-08	1
NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+	5.32E-08	1
NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+	5.32E-08	1
NFE2L1	chr17	46125824	+	NPEPPS	chr17	45673718	+	5.32E-08	1

Distribution 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.

Distribution 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 NFE2L1-NPEPPS

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:46125824/:45673719)
- 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
NFE2L1 Q14494	NPEPPS P55786
FUNCTION: [Endoplasmic reticulum membrane sensor NFE2L1]: Endoplasmic reticulum membrane sensor that translocates into the nucleus in response to various stresses to act as a transcription factor (PubMed:20932482, PubMed:24448410). Constitutes a precursor of the transcription factor NRF1 (By similarity). Able to detect various cellular stresses, such as cholesterol excess, oxidative stress or proteasome inhibition (PubMed:20932482). In response to stress, it is released from the endoplasmic reticulum membrane following cleavage by the protease DDI2 and translocates into the nucleus to form the transcription factor NRF1 (By similarity). Acts as a key sensor of cholesterol excess: in excess cholesterol conditions, the endoplasmic reticulum membrane form of the protein directly binds cholesterol via its CRAC motif, preventing cleavage and release of the transcription factor NRF1, thereby allowing expression of genes promoting cholesterol removal, such as CD36 (By similarity). Involved in proteasome homeostasis: in response to proteasome inhibition, it is released from the endoplasmic reticulum membrane, translocates to the nucleus and activates expression of genes encoding proteasome subunits (PubMed:20932482). {ECO:0000250\|UniProtKB:Q61985, ECO:0000269\|PubMed:20932482, ECO:0000269\|PubMed:24448410}.; FUNCTION: [Transcription factor NRF1]: CNC-type bZIP family transcription factor that translocates to the nucleus and regulates expression of target genes in response to various stresses (PubMed:8932385, PubMed:9421508). Heterodimerizes with small-Maf proteins (MAFF, MAFG or MAFK) and binds DNA motifs including the antioxidant response elements (AREs), which regulate expression of genes involved in oxidative stress response (PubMed:8932385, PubMed:9421508). Activates or represses expression of target genes, depending on the context (PubMed:8932385, PubMed:9421508). Plays a key role in cholesterol homeostasis by acting as a sensor of cholesterol excess: in low cholesterol conditions, translocates into the nucleus and represses expression of genes involved in defense against cholesterol excess, such as CD36 (By similarity). In excess cholesterol conditions, the endoplasmic reticulum membrane form of the protein directly binds cholesterol via its CRAC motif, preventing cleavage and release of the transcription factor NRF1, thereby allowing expression of genes promoting cholesterol removal (By similarity). Critical for redox balance in response to oxidative stress: acts by binding the AREs motifs on promoters and mediating activation of oxidative stress response genes, such as GCLC, GCLM, GSS, MT1 and MT2 (By similarity). Plays an essential role during fetal liver hematopoiesis: probably has a protective function against oxidative stress and is involved in lipid homeostasis in the liver (By similarity). Involved in proteasome homeostasis: in response to proteasome inhibition, mediates the 'bounce-back' of proteasome subunits by translocating into the nucleus and activating expression of genes encoding proteasome subunits (PubMed:20932482). Also involved in regulating glucose flux (By similarity). Together with CEBPB; represses expression of DSPP during odontoblast differentiation (PubMed:15308669). In response to ascorbic acid induction, activates expression of SP7/Osterix in osteoblasts. {ECO:0000250\|UniProtKB:Q61985, ECO:0000269\|PubMed:15308669, ECO:0000269\|PubMed:20932482, ECO:0000269\|PubMed:8932385, ECO:0000269\|PubMed:9421508}.	FUNCTION: Aminopeptidase with broad substrate specificity for several peptides. Involved in proteolytic events essential for cell growth and viability. May act as regulator of neuropeptide activity. Plays a role in the antigen-processing pathway for MHC class I molecules. Involved in the N-terminal trimming of cytotoxic T-cell epitope precursors. Digests the poly-Q peptides found in many cellular proteins. Digests tau from normal brain more efficiently than tau from Alzheimer disease brain. {ECO:0000269\|PubMed:10978616, ECO:0000269\|PubMed:11062501, ECO:0000269\|PubMed:17154549, ECO:0000269\|PubMed:17318184, ECO:0000269\|PubMed:19917696}.

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.

- In-frame and 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

- In-frame and 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

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Fusion Gene Sequence for NFE2L1-NPEPPS

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 NFE2L1-NPEPPS

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for NFE2L1-NPEPPS

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for NFE2L1-NPEPPS

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source