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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:NLGN1-FNDC3B (FusionGDB2 ID:59304)

Fusion Gene Summary for NLGN1-FNDC3B

check button Fusion gene summary
Fusion gene informationFusion gene name: NLGN1-FNDC3B
Fusion gene ID: 59304
HgeneTgene
Gene symbol

NLGN1

FNDC3B

Gene ID

22871

64778

Gene nameneuroligin 1fibronectin type III domain containing 3B
SynonymsNL1FAD104|PRO4979|YVTM2421
Cytomap

3q26.31

3q26.31

Type of geneprotein-codingprotein-coding
Descriptionneuroligin-1fibronectin type III domain-containing protein 3BHCV NS5A-binding protein 37factor for adipocyte differentiation 104
Modification date2020031320200313
UniProtAcc

Q8N2Q7

Q53EP0

Ensembl transtripts involved in fusion geneENST00000457714, ENST00000361589, 
ENST00000401917, ENST00000466350, 
ENST00000545397, 		ENST00000336824, 
ENST00000415807, ENST00000416957, 
ENST00000392699, ENST00000421757, 
ENST00000423424, ENST00000476794, 
Fusion gene scores* DoF score12 X 9 X 6=64821 X 23 X 11=5313
# samples 1228
** MAII scorelog2(12/648*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/5313*10)=-4.2460279805281
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NLGN1 [Title/Abstract] AND FNDC3B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFNDC3B(171944737)-NLGN1(173993105), # samples:3
NLGN1(173152868)-FNDC3B(172080423), # samples:1
Anticipated loss of major functional domain due to fusion event.FNDC3B-NLGN1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgeneNLGN1

GO:0031175

neuron projection development

22750515

HgeneNLGN1

GO:0051965

positive regulation of synapse assembly

24613359


check buttonFusion gene breakpoints across NLGN1 (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 FNDC3B (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
ChimerDB4SKCMTCGA-YD-A9TA-06ANLGN1chr3

173152868

+FNDC3Bchr3

172080423

+


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Fusion Gene ORF analysis for NLGN1-FNDC3B

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
5UTR-3CDSENST00000457714ENST00000336824NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
5UTR-3CDSENST00000457714ENST00000415807NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
5UTR-3CDSENST00000457714ENST00000416957NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
5UTR-intronENST00000457714ENST00000392699NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
5UTR-intronENST00000457714ENST00000421757NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
5UTR-intronENST00000457714ENST00000423424NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
5UTR-intronENST00000457714ENST00000476794NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000361589ENST00000336824NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000361589ENST00000415807NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000361589ENST00000416957NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000401917ENST00000336824NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000401917ENST00000415807NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000401917ENST00000416957NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000466350ENST00000336824NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000466350ENST00000415807NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000466350ENST00000416957NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000545397ENST00000336824NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000545397ENST00000415807NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-3CDSENST00000545397ENST00000416957NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000361589ENST00000392699NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000361589ENST00000421757NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000361589ENST00000423424NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000361589ENST00000476794NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000401917ENST00000392699NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000401917ENST00000421757NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000401917ENST00000423424NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000401917ENST00000476794NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000466350ENST00000392699NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000466350ENST00000421757NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000466350ENST00000423424NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000466350ENST00000476794NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000545397ENST00000392699NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000545397ENST00000421757NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000545397ENST00000423424NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+
intron-intronENST00000545397ENST00000476794NLGN1chr3

173152868

+FNDC3Bchr3

172080423

+

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 NLGN1-FNDC3B


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)
NLGN1chr3173152868+FNDC3Bchr3172080422+0.0048492690.9951507
NLGN1chr3173152868+FNDC3Bchr3172080422+0.0048492690.9951507

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.
genomic feature of top 1%

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Fusion Protein Features for NLGN1-FNDC3B


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/:171944737/:173993105)
- 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
NLGN1

Q8N2Q7

FNDC3B

Q53EP0

FUNCTION: Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and probably mediates its effects by recruiting and clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses. Required to maintain wakefulness quality and normal synchrony of cerebral cortex activity during wakefulness and sleep (By similarity). The protein is involved in nervous system development. {ECO:0000250|UniProtKB:Q99K10, ECO:0000269|PubMed:28841651}.FUNCTION: May be a positive regulator of adipogenesis. {ECO:0000269|PubMed:15564382}.

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 NLGN1-FNDC3B


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 NLGN1-FNDC3B


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 NLGN1-FNDC3B


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 NLGN1-FNDC3B


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