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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:PTEN-EMX2 (FusionGDB2 ID:69912)

Fusion Gene Summary for PTEN-EMX2

check button Fusion gene summary
Fusion gene informationFusion gene name: PTEN-EMX2
Fusion gene ID: 69912
HgeneTgene
Gene symbol

PTEN

EMX2

Gene ID

5728

2018

Gene namephosphatase and tensin homologempty spiracles homeobox 2
Synonyms10q23del|BZS|CWS1|DEC|GLM2|MHAM|MMAC1|PTEN1|PTENbeta|TEP1-
Cytomap

10q23.31

10q26.11

Type of geneprotein-codingprotein-coding
Descriptionphosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTENMMAC1 phosphatase and tensin homolog deleted on chromosome 10PTENepsilonmitochondrial PTENalphamitochondrial phosphatase and tensin protein alphamutathomeobox protein EMX2empty spiracles homolog 2empty spiracles-like protein 2
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000371953, ENST00000472832, 
ENST00000546446, ENST00000442245, 
ENST00000553456, 
Fusion gene scores* DoF score32 X 22 X 15=105602 X 4 X 2=16
# samples 422
** MAII scorelog2(42/10560*10)=-4.65207669657969
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/16*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PTEN [Title/Abstract] AND EMX2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTEN(89653866)-EMX2(119305142), # samples:1
PTEN(89653866)-EMX2(119305143), # samples:1
PTEN(89653866)-EMX2(119307576), # samples:1
Anticipated loss of major functional domain due to fusion event.PTEN-EMX2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PTEN-EMX2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
PTEN-EMX2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PTEN-EMX2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PTEN-EMX2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
HgenePTEN

GO:0001933

negative regulation of protein phosphorylation

20123964

HgenePTEN

GO:0006470

protein dephosphorylation

9256433

HgenePTEN

GO:0008285

negative regulation of cell proliferation

19057511

HgenePTEN

GO:0045736

negative regulation of cyclin-dependent protein serine/threonine kinase activity

21241890

HgenePTEN

GO:0046855

inositol phosphate dephosphorylation

9593664

HgenePTEN

GO:0046856

phosphatidylinositol dephosphorylation

9593664|9811831

HgenePTEN

GO:0050821

protein stabilization

20123964

HgenePTEN

GO:0060070

canonical Wnt signaling pathway

20123964

HgenePTEN

GO:1902807

negative regulation of cell cycle G1/S phase transition

10918569

HgenePTEN

GO:1904668

positive regulation of ubiquitin protein ligase activity

21241890

HgenePTEN

GO:2000060

positive regulation of ubiquitin-dependent protein catabolic process

21241890

HgenePTEN

GO:2000134

negative regulation of G1/S transition of mitotic cell cycle

21241890


check buttonFusion gene breakpoints across PTEN (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across EMX2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4LUSCTCGA-94-7557PTENchr10

89653866

+EMX2chr10

119305142

+
ChimerDB4LUSCTCGA-94-7557PTENchr10

89653866

+EMX2chr10

119305143

+
ChimerDB4LUSCTCGA-94-7557PTENchr10

89653866

+EMX2chr10

119307576

+


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Fusion Gene ORF analysis for PTEN-EMX2

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-3UTRENST00000371953ENST00000546446PTENchr10

89653866

+EMX2chr10

119305142

+
5CDS-3UTRENST00000371953ENST00000546446PTENchr10

89653866

+EMX2chr10

119305143

+
5CDS-3UTRENST00000371953ENST00000546446PTENchr10

89653866

+EMX2chr10

119307576

+
5CDS-intronENST00000371953ENST00000442245PTENchr10

89653866

+EMX2chr10

119305142

+
5CDS-intronENST00000371953ENST00000442245PTENchr10

89653866

+EMX2chr10

119305143

+
Frame-shiftENST00000371953ENST00000553456PTENchr10

89653866

+EMX2chr10

119305142

+
Frame-shiftENST00000371953ENST00000553456PTENchr10

89653866

+EMX2chr10

119305143

+
Frame-shiftENST00000371953ENST00000553456PTENchr10

89653866

+EMX2chr10

119307576

+
In-frameENST00000371953ENST00000442245PTENchr10

89653866

+EMX2chr10

119307576

+
intron-3CDSENST00000472832ENST00000442245PTENchr10

89653866

+EMX2chr10

119307576

+
intron-3CDSENST00000472832ENST00000553456PTENchr10

89653866

+EMX2chr10

119305142

+
intron-3CDSENST00000472832ENST00000553456PTENchr10

89653866

+EMX2chr10

119305143

+
intron-3CDSENST00000472832ENST00000553456PTENchr10

89653866

+EMX2chr10

119307576

+
intron-3UTRENST00000472832ENST00000546446PTENchr10

89653866

+EMX2chr10

119305142

+
intron-3UTRENST00000472832ENST00000546446PTENchr10

89653866

+EMX2chr10

119305143

+
intron-3UTRENST00000472832ENST00000546446PTENchr10

89653866

+EMX2chr10

119307576

+
intron-intronENST00000472832ENST00000442245PTENchr10

89653866

+EMX2chr10

119305142

+
intron-intronENST00000472832ENST00000442245PTENchr10

89653866

+EMX2chr10

119305143

+

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)
ENST00000371953PTENchr1089653866+ENST00000442245EMX2chr10119307576+235815215561524322

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
ENST00000371953ENST00000442245PTENchr1089653866+EMX2chr10119307576+0.63635750.36364257

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Fusion Genomic Features for PTEN-EMX2


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)
PTENchr1089653866+EMX2chr10119307575+0.0006995420.9993005
PTENchr1089653866+EMX2chr10119305142+2.93E-050.9999707
PTENchr1089653866+EMX2chr10119307575+0.0006995420.9993005
PTENchr1089653866+EMX2chr10119305142+2.93E-050.9999707

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.
genomic feature

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 PTEN-EMX2


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/chr10:89653866/chr10:119305142)
- 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
..
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: 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}.

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
TgeneEMX2chr10:89653866chr10:119307576ENST0000044224502154_213135170.0DNA bindingHomeobox

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePTENchr10:89653866chr10:119307576ENST00000371953+2914_18554404.0DomainPhosphatase tensin-type
HgenePTENchr10:89653866chr10:119307576ENST00000371953+29190_35054404.0DomainC2 tensin-type
HgenePTENchr10:89653866chr10:119307576ENST00000371953+29401_40354404.0RegionNote=PDZ domain-binding
TgeneEMX2chr10:89653866chr10:119307576ENST000004422450254_59135170.0Compositional biasNote=Poly-Ala
TgeneEMX2chr10:89653866chr10:119307576ENST000005534561354_59197253.0Compositional biasNote=Poly-Ala
TgeneEMX2chr10:89653866chr10:119307576ENST0000055345613154_213197253.0DNA bindingHomeobox


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Fusion Gene Sequence for PTEN-EMX2


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.
>69912_69912_1_PTEN-EMX2_PTEN_chr10_89653866_ENST00000371953_EMX2_chr10_119307576_ENST00000442245_length(transcript)=2358nt_BP=1521nt
GGTAACCTCAGACTCGAGTCAGTGACACTGCTCAACGCACCCATCTCAGCTTTCATCATCAGTCCTCCACCCCCGCCCCACAACAGCCTA
CCCTGCCTCCGGCTGGGTTTCTGGGCAGAGGCCGAGGCTTAGCTCGTTATCCTCGCCTCGCGTTGCTGCAAAAGCCGCAGCAAGTGCAGC
TGCAGGCTGGCGGCTGGGAACCGGCCCGAGCAAGCCCCAGGCAGCTACACTGGGCATGCTCAGTAGAGCCTGCGGCTTGGGGACTCTGCG
CTCGCACCCAGAGCTACCGCTCTGCCCCCTCCTACCGCCCCCTGCCCTGCCCTGCCCTCCCCTCGCCCGGCGCGGTCCCGTCCGCCTCTC
GCTCGCCTCCCGCCTCCCCTCGGTCTTCCGAGGCGCCCGGGCTCCCGGCGCGGCGGCGGAGGGGGCGGGCAGGCCGGCGGGCGGTGATGT
GGCGGGACTCTTTATGCGCTGCGGCAGGATACGCGCTCGGCGCTGGGACGCGACTGCGCTCAGTTCTCTCCTCTCGGAAGCTGCAGCCAT
GATGGAAGTTTGAGAGTTGAGCCGCTGTGAGGCGAGGCCGGGCTCAGGCGAGGGAGATGAGAGACGGCGGCGGCCGCGGCCCGGAGCCCC
TCTCAGCGCCTGTGAGCAGCCGCGGGGGCAGCGCCCTCGGGGAGCCGGCCGGCCTGCGGCGGCGGCAGCGGCGGCGTTTCTCGCCTCCTC
TTCGTCTTTTCTAACCGTGCAGCCTCTTCCTCGGCTTCTCCTGAAAGGGAAGGTGGAAGCCGTGGGCTCGGGCGGGAGCCGGCTGAGGCG
CGGCGGCGGCGGCGGCACCTCCCGCTCCTGGAGCGGGGGGGAGAAGCGGCGGCGGCGGCGGCCGCGGCGGCTGCAGCTCCAGGGAGGGGG
TCTGAGTCGCCTGTCACCATTTCCAGGGCTGGGAACGCCGGAGAGTTGGTCTCTCCCCTTCTACTGCCTCCAACACGGCGGCGGCGGCGG
CTGGCACATCCAGGGACCCGGGCCGGTTTTAAACCTCCCGTGCGCCGCCGCCGCACCCCCCGTGGCCCGGGCTCCGGAGGCCGCCGGCGG
AGGCAGCCGTTCGGAGGATTATTCGTCTTCTCCCCATTCCGCTGCCGCCGCTGCCAGGCCTCTGGCTGCTGAGGAGAAGCAGGCCCAGTC
GCTGCAACCATCCAGCAGCCGCCGCAGCAGCCATTACCCGGCTGCGGTCCAGAGCCAAGCGGCGGCAGAGCGAGGGGCATCAGCTACCGC
CAAGTCCAGAGCCATTTCCATCCTGCAGAAGAAGCCCCGCCACCAGCAGCTTCTGCCATCTCTCTCCTCCTTTTTCTTCAGCCACAGGCT
CCCAGACATGACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTATAT
TTATCCAAACATTATTGCTATGGGATTTCCTGCAGAAAGACTTGAAGGCGTATACAGGAACAATATTGATGATGTAGTAAGGTAAAAGTA
TGGTTTCAGAACCGAAGAACAAAGTTCAAAAGGCAGAAGCTGGAGGAAGAAGGCTCAGATTCGCAACAAAAGAAAAAAGGGACGCACCAT
ATTAACCGGTGGAGAATCGCCACCAAGCAGGCGAGTCCGGAGGAAATAGACGTGACCTCAGATGATTAAAAACATAAACCTAACCCCACA
GAAACGGACAACATGGAGCAAAAGAGACAGGGAGAGGTGGAGAAGGAAAAAACCCTACAAAACAAAAACAAACCGCATACACGTTCACCG
AGAAAGGGAGAGGGAATCGGAGGGAGCAGCGGAATGCGGCGAAGACTCTGGACAGCGAGGGCACAGGGTCCCAAACCGAGGCCGCGCCAA
GATGGCAGAGGATGGAGGCTCCTTCATCAACAAGCGACCCTCGTCTAAAGAGGCAGCTGAGTGAGAGACACAGAGAGAAGGAGAAAGAGG
GAGGGAGAGAGAGAAAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAAAGCTGAACGTGCACTCTGACAAGGGGAGCTGTCAATCAA
ACACCAAACCGGGGAGACAAGATGATTGGCAGGTATTCCGTTTATCACAGTCCACTTAAAAAATGATGATGATGATAAAAACCACGACCC
AACCAGGCACAGGACTTTTTTGTTTTTTGCACTTCGCTGTGTTTCCCCCCCATCTTTAAAAATAATTAGTAATAAAAAACAAAAATTCCA
TATCTAGCCCCATCCCACACCTGTTTCAAATCCTTGAAATGCATGTAGCAGTTGTTGGGCGAATGGTGTTTAAAGACCGAAAATGAATTG

>69912_69912_1_PTEN-EMX2_PTEN_chr10_89653866_ENST00000371953_EMX2_chr10_119307576_ENST00000442245_length(amino acids)=322AA_BP=
MSRCEARPGSGEGDERRRRPRPGAPLSACEQPRGQRPRGAGRPAAAAAAAFLASSSSFLTVQPLPRLLLKGKVEAVGSGGSRLRRGGGGG
TSRSWSGGEKRRRRRPRRLQLQGGGLSRLSPFPGLGTPESWSLPFYCLQHGGGGGWHIQGPGPVLNLPCAAAAPPVARAPEAAGGGSRSE
DYSSSPHSAAAAARPLAAEEKQAQSLQPSSSRRSSHYPAAVQSQAAAERGASATAKSRAISILQKKPRHQQLLPSLSSFFFSHRLPDMTA

--------------------------------------------------------------

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Fusion Gene PPI Analysis for PTEN-EMX2


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 PTEN-EMX2


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 PTEN-EMX2


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