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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:PHTF2-NAP1L1 (FusionGDB2 ID:65024)

Fusion Gene Summary for PHTF2-NAP1L1

check button Fusion gene summary
Fusion gene informationFusion gene name: PHTF2-NAP1L1
Fusion gene ID: 65024
HgeneTgene
Gene symbol

PHTF2

NAP1L1

Gene ID

57157

4673

Gene nameputative homeodomain transcription factor 2nucleosome assembly protein 1 like 1
Synonyms-NAP1|NAP1L|NRP
Cytomap

7q11.23-q21.11

12q21.2

Type of geneprotein-codingprotein-coding
Descriptionputative homeodomain transcription factor 2nucleosome assembly protein 1-like 1HSP22-like protein interacting proteinNAP-1-related protein
Modification date2020031320200322
UniProtAcc.

P55209

Ensembl transtripts involved in fusion geneENST00000275575, ENST00000307305, 
ENST00000415251, ENST00000422959, 
ENST00000424760, ENST00000248550, 
ENST00000416283, ENST00000450574, 
ENST00000454592, 		ENST00000261182, 
ENST00000393263, ENST00000431879, 
ENST00000547773, ENST00000535020, 
ENST00000542344, ENST00000544816, 
ENST00000549596, ENST00000547993, 
ENST00000548044, ENST00000552342, 
Fusion gene scores* DoF score8 X 7 X 6=33618 X 20 X 6=2160
# samples 922
** MAII scorelog2(9/336*10)=-1.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/2160*10)=-3.29545588352617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PHTF2 [Title/Abstract] AND NAP1L1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPHTF2(77428288)-NAP1L1(76454059), # 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

check buttonFusion gene breakpoints across PHTF2 (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 NAP1L1 (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-D7-8574-01APHTF2chr7

77428288

+NAP1L1chr12

76454059

-


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Fusion Gene ORF analysis for PHTF2-NAP1L1

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-3CDSENST00000275575ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000275575ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000275575ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000275575ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000307305ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000307305ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000307305ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000307305ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000415251ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000415251ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000415251ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000415251ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000422959ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000422959ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000422959ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000422959ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000424760ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000424760ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000424760ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-3CDSENST00000424760ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000275575ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000275575ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000275575ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000275575ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000307305ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000307305ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000307305ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000307305ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000415251ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000415251ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000415251ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000415251ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000422959ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000422959ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000422959ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000422959ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000424760ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000424760ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000424760ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-5UTRENST00000424760ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000275575ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000275575ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000275575ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000307305ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000307305ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000307305ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000415251ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000415251ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000415251ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000422959ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000422959ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000422959ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000424760ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000424760ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
5UTR-intronENST00000424760ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000248550ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000248550ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000248550ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000248550ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000416283ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000416283ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000416283ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000416283ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000450574ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000450574ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000450574ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000450574ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000454592ENST00000261182PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000454592ENST00000393263PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000454592ENST00000431879PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-3CDSENST00000454592ENST00000547773PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000248550ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000248550ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000248550ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000248550ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000416283ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000416283ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000416283ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000416283ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000450574ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000450574ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000450574ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000450574ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000454592ENST00000535020PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000454592ENST00000542344PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000454592ENST00000544816PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-5UTRENST00000454592ENST00000549596PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000248550ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000248550ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000248550ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000416283ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000416283ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000416283ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000450574ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000450574ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000450574ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000454592ENST00000547993PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000454592ENST00000548044PHTF2chr7

77428288

+NAP1L1chr12

76454059

-
intron-intronENST00000454592ENST00000552342PHTF2chr7

77428288

+NAP1L1chr12

76454059

-

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 PHTF2-NAP1L1


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 PHTF2-NAP1L1


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/:77428288/:76454059)
- 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
.NAP1L1

P55209

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Histone chaperone that plays a role in the nuclear import of H2A-H2B and nucleosome assembly (PubMed:20002496, PubMed:26841755). Participates also in several important DNA repair mechanisms: greatly enhances ERCC6-mediated chromatin remodeling which is essential for transcription-coupled nucleotide excision DNA repair (PubMed:28369616). Stimulates also homologous recombination (HR) by RAD51 and RAD54 which is essential in mitotic DNA double strand break (DSB) repair (PubMed:24798879). Plays a key role in the regulation of embryonic neurogenesis (By similarity). Promotes the proliferation of neural progenitors and inhibits neuronal differentiation during cortical development (By similarity). Regulates neurogenesis via the modulation of RASSF10; regulates RASSF10 expression by promoting SETD1A-mediated H3K4 methylation at the RASSF10 promoter (By similarity). {ECO:0000250|UniProtKB:P28656, ECO:0000269|PubMed:20002496, ECO:0000269|PubMed:24798879, ECO:0000269|PubMed:26841755, ECO:0000269|PubMed:28369616}.; FUNCTION: (Microbial infection) Positively regulates Epstein-Barr virus reactivation in epithelial cells through the induction of viral BZLF1 expression. {ECO:0000269|PubMed:23691099}.; FUNCTION: (Microbial infection) Together with human herpesvirus 8 protein LANA1, assists the proper assembly of the nucleosome on the replicated viral DNA. {ECO:0000269|PubMed:27599637}.

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 PHTF2-NAP1L1


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 PHTF2-NAP1L1


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 PHTF2-NAP1L1


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 PHTF2-NAP1L1


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