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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:NEO1-PML (FusionGDB2 ID:58620)

Fusion Gene Summary for NEO1-PML

check button Fusion gene summary
Fusion gene informationFusion gene name: NEO1-PML
Fusion gene ID: 58620
HgeneTgene
Gene symbol

NEO1

PML

Gene ID

4756

5371

Gene nameneogenin 1promyelocytic leukemia
SynonymsIGDCC2|NGN|NTN1R2MYL|PP8675|RNF71|TRIM19
Cytomap

15q24.1

15q24.1

Type of geneprotein-codingprotein-coding
Descriptionneogeninimmunoglobulin superfamily DCC subclass member 2neogenin homolog 1protein PMLPML/RARA fusionRING finger protein 71probable transcription factor PMLpromyelocytic leukemia proteinpromyelocytic leukemia, inducer oftripartite motif protein TRIM19tripartite motif-containing protein 19
Modification date2020031320200313
UniProtAcc

Q92859

PRAM1

Ensembl transtripts involved in fusion geneENST00000261908, ENST00000339362, 
ENST00000558964, ENST00000560262, 
ENST00000560352, 		ENST00000569161, 
ENST00000268058, ENST00000268059, 
ENST00000354026, ENST00000359928, 
ENST00000395132, ENST00000395135, 
ENST00000435786, ENST00000436891, 
ENST00000563500, ENST00000564428, 
ENST00000565898, ENST00000567543, 
ENST00000569477, ENST00000569965, 
Fusion gene scores* DoF score14 X 7 X 7=6869 X 24 X 6=1296
# samples 1528
** MAII scorelog2(15/686*10)=-2.19324607567693
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/1296*10)=-2.21056698593966
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NEO1 [Title/Abstract] AND PML [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNEO1(73345146)-PML(74315169), # samples:1
Anticipated loss of major functional domain due to fusion event.NEO1-PML seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
NEO1-PML seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
NEO1-PML seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
NEO1-PML seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgenePML

GO:0001666

response to hypoxia

16915281

TgenePML

GO:0030308

negative regulation of cell growth

9448006

TgenePML

GO:0034097

response to cytokine

9412458

TgenePML

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

22406621

TgenePML

GO:0045087

innate immune response

18248090

TgenePML

GO:0045892

negative regulation of transcription, DNA-templated

9448006

TgenePML

GO:0051457

maintenance of protein location in nucleus

17332504

TgenePML

GO:0065003

protein-containing complex assembly

12915590

TgenePML

GO:0090398

cellular senescence

22002537|22117195|23431171

TgenePML

GO:1902187

negative regulation of viral release from host cell

18248090


check buttonFusion gene breakpoints across NEO1 (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 PML (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
ChimerDB4STADTCGA-BR-8366-01ANEO1chr15

73345146

+PMLchr15

74315169

+


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Fusion Gene ORF analysis for NEO1-PML

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-intronENST00000261908ENST00000569161NEO1chr15

73345146

+PMLchr15

74315169

+
5CDS-intronENST00000339362ENST00000569161NEO1chr15

73345146

+PMLchr15

74315169

+
5CDS-intronENST00000558964ENST00000569161NEO1chr15

73345146

+PMLchr15

74315169

+
5CDS-intronENST00000560262ENST00000569161NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000268058NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000268059NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000354026NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000359928NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000395132NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000395135NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000435786NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000436891NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000563500NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000564428NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000565898NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000567543NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000569477NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000261908ENST00000569965NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000268058NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000268059NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000354026NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000359928NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000395132NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000395135NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000435786NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000436891NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000563500NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000564428NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000565898NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000567543NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000569477NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000339362ENST00000569965NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000268058NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000268059NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000354026NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000359928NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000395132NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000395135NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000435786NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000436891NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000563500NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000564428NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000565898NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000567543NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000569477NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000558964ENST00000569965NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000268058NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000268059NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000354026NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000359928NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000395132NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000395135NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000435786NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000436891NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000563500NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000564428NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000565898NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000567543NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000569477NEO1chr15

73345146

+PMLchr15

74315169

+
Frame-shiftENST00000560262ENST00000569965NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000268058NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000268059NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000354026NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000359928NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000395132NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000395135NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000435786NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000436891NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000563500NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000564428NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000565898NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000567543NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000569477NEO1chr15

73345146

+PMLchr15

74315169

+
intron-3CDSENST00000560352ENST00000569965NEO1chr15

73345146

+PMLchr15

74315169

+
intron-intronENST00000560352ENST00000569161NEO1chr15

73345146

+PMLchr15

74315169

+

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 NEO1-PML


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)
NEO1chr1573345146+PMLchr1574315168+1.98E-091
NEO1chr1573345146+PMLchr1574315168+1.98E-091

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 NEO1-PML


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/:73345146/:74315169)
- 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
NEO1

Q92859

PML

PRAM1

FUNCTION: Multi-functional cell surface receptor regulating cell adhesion in many diverse developmental processes, including neural tube and mammary gland formation, myogenesis and angiogenesis. Receptor for members of the BMP, netrin, and repulsive guidance molecule (RGM) families. Netrin-Neogenin interactions result in a chemoattractive axon guidance response and cell-cell adhesion, the interaction between NEO1/Neogenin and RGMa and RGMb induces a chemorepulsive response. {ECO:0000269|PubMed:21149453}.670

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 NEO1-PML


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 NEO1-PML


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 NEO1-PML


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 NEO1-PML


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