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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:FOS-NF1 (FusionGDB2 ID:31037)

Fusion Gene Summary for FOS-NF1

check button Fusion gene summary
Fusion gene informationFusion gene name: FOS-NF1
Fusion gene ID: 31037
HgeneTgene
Gene symbol

FOS

NF1

Gene ID

2353

4763

Gene nameFos proto-oncogene, AP-1 transcription factor subunitneurofibromin 1
SynonymsAP-1|C-FOS|p55NFNS|VRNF|WSS
Cytomap

14q24.3

17q11.2

Type of geneprotein-codingprotein-coding
Descriptionproto-oncogene c-FosFBJ murine osteosarcoma viral (v-fos) oncogene homolog (oncogene FOS)FBJ murine osteosarcoma viral oncogene homologFos proto-oncogene, AP-1 trancription factor subunitG0/G1 switch regulatory protein 7activator protein 1cellular oneurofibrominneurofibromatosis 1neurofibromatosis-related protein NF-1truncated neurofibromin 1
Modification date2020032920200322
UniProtAcc

P01100

P21359

Ensembl transtripts involved in fusion geneENST00000303562, ENST00000535987, 
ENST00000554617, ENST00000555242, 
ENST00000555347, ENST00000555686, 
ENST00000556324, 		ENST00000356175, 
ENST00000358273, ENST00000417592, 
ENST00000431387, ENST00000444181, 
ENST00000581113, 
Fusion gene scores* DoF score6 X 9 X 1=5428 X 30 X 15=12600
# samples 933
** MAII scorelog2(9/54*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(33/12600*10)=-5.25481389902883
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FOS [Title/Abstract] AND NF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFOS(75748933)-NF1(29581290), # 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
HgeneFOS

GO:0007179

transforming growth factor beta receptor signaling pathway

9732876

HgeneFOS

GO:0034614

cellular response to reactive oxygen species

17217916

HgeneFOS

GO:0045893

positive regulation of transcription, DNA-templated

9732876

HgeneFOS

GO:0045944

positive regulation of transcription by RNA polymerase II

10508860

HgeneFOS

GO:0060395

SMAD protein signal transduction

9732876

TgeneNF1

GO:0043547

positive regulation of GTPase activity

2121371


check buttonFusion gene breakpoints across FOS (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 NF1 (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
ChiTaRS5.0N/AGW493447FOSchr14

75748933

+NF1chr17

29581290

+


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Fusion Gene ORF analysis for FOS-NF1

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-intronENST00000303562ENST00000356175FOSchr14

75748933

+NF1chr17

29581290

+
5CDS-intronENST00000303562ENST00000358273FOSchr14

75748933

+NF1chr17

29581290

+
5CDS-intronENST00000303562ENST00000417592FOSchr14

75748933

+NF1chr17

29581290

+
5CDS-intronENST00000303562ENST00000431387FOSchr14

75748933

+NF1chr17

29581290

+
5CDS-intronENST00000303562ENST00000444181FOSchr14

75748933

+NF1chr17

29581290

+
5CDS-intronENST00000303562ENST00000581113FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000535987ENST00000356175FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000535987ENST00000358273FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000535987ENST00000417592FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000535987ENST00000431387FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000535987ENST00000444181FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000535987ENST00000581113FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000554617ENST00000356175FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000554617ENST00000358273FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000554617ENST00000417592FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000554617ENST00000431387FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000554617ENST00000444181FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000554617ENST00000581113FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555242ENST00000356175FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555242ENST00000358273FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555242ENST00000417592FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555242ENST00000431387FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555242ENST00000444181FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555242ENST00000581113FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555347ENST00000356175FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555347ENST00000358273FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555347ENST00000417592FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555347ENST00000431387FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555347ENST00000444181FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555347ENST00000581113FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555686ENST00000356175FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555686ENST00000358273FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555686ENST00000417592FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555686ENST00000431387FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555686ENST00000444181FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000555686ENST00000581113FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000556324ENST00000356175FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000556324ENST00000358273FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000556324ENST00000417592FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000556324ENST00000431387FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000556324ENST00000444181FOSchr14

75748933

+NF1chr17

29581290

+
intron-intronENST00000556324ENST00000581113FOSchr14

75748933

+NF1chr17

29581290

+

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 FOS-NF1


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 FOS-NF1


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/:75748933/:29581290)
- 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
FOS

P01100

NF1

P21359

FUNCTION: Nuclear phosphoprotein which forms a tight but non-covalently linked complex with the JUN/AP-1 transcription factor. In the heterodimer, FOS and JUN/AP-1 basic regions each seems to interact with symmetrical DNA half sites. On TGF-beta activation, forms a multimeric SMAD3/SMAD4/JUN/FOS complex at the AP1/SMAD-binding site to regulate TGF-beta-mediated signaling. Has a critical function in regulating the development of cells destined to form and maintain the skeleton. It is thought to have an important role in signal transduction, cell proliferation and differentiation. In growing cells, activates phospholipid synthesis, possibly by activating CDS1 and PI4K2A. This activity requires Tyr-dephosphorylation and association with the endoplasmic reticulum. {ECO:0000269|PubMed:16055710, ECO:0000269|PubMed:17160021, ECO:0000269|PubMed:22105363, ECO:0000269|PubMed:7588633, ECO:0000269|PubMed:9732876}.FUNCTION: Stimulates the GTPase activity of Ras. NF1 shows greater affinity for Ras GAP, but lower specific activity. May be a regulator of Ras activity. {ECO:0000269|PubMed:2121371, ECO:0000269|PubMed:8417346}.

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 FOS-NF1


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 FOS-NF1


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 FOS-NF1


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 FOS-NF1


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