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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:NBEA-POSTN

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NBEA-POSTN
FusionPDB ID: 57430
FusionGDB2.0 ID: 57430
HgeneTgene
Gene symbol

NBEA

POSTN

Gene ID

26960

10631

Gene nameneurobeachinperiostin
SynonymsBCL8B|LYST2OSF-2|OSF2|PDLPOSTN|PN
Cytomap

13q13.3

13q13.3

Type of geneprotein-codingprotein-coding
Descriptionneurobeachinlysosomal-trafficking regulator 2periostinosteoblast specific factor 2 (fasciclin I-like)periodontal ligament-specific periostinperiostin, osteoblast specific factor
Modification date2020032820200313
UniProtAcc

Q6ZNJ1

Main function of 5'-partner protein: FUNCTION: Probably involved in thrombopoiesis. Plays a role in the development or secretion of alpha-granules, that contain several growth factors important for platelet biogenesis. {ECO:0000269|PubMed:21765411, ECO:0000269|PubMed:21765412}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000310336, ENST00000379939, 
ENST00000400445, ENST00000540320, 
ENST00000379922, ENST00000461581, 
ENST00000537702, 		ENST00000497145, 
ENST00000379742, ENST00000379743, 
ENST00000379747, ENST00000379749, 
ENST00000541179, ENST00000541481, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 15 X 7=157512 X 12 X 3=432
# samples 1512
** MAII scorelog2(15/1575*10)=-3.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/432*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: NBEA [Title/Abstract] AND POSTN [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: NBEA [Title/Abstract] AND POSTN [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NBEA(35883729)-POSTN(38171419), # samples:1
Anticipated loss of major functional domain due to fusion event.NBEA-POSTN seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
NBEA-POSTN seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
NBEA-POSTN seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
NBEA-POSTN seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
TgenePOSTN

GO:0007155

cell adhesion

12235007

TgenePOSTN

GO:0071307

cellular response to vitamin K

18450759



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/chr13:35883729/chr13:38171419)
- 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 buttonRetention analysis results 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, are available here.

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


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Fusion Amino Acid Sequences


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000540320NBEAchr1335883729-ENST00000541179POSTNchr1338171419-9414643742086632747
ENST00000540320NBEAchr1335883729-ENST00000379749POSTNchr1338171419-9493643742087442774
ENST00000540320NBEAchr1335883729-ENST00000379747POSTNchr1338171419-9573643742088282802
ENST00000540320NBEAchr1335883729-ENST00000379743POSTNchr1338171419-9490643742087472775
ENST00000540320NBEAchr1335883729-ENST00000379742POSTNchr1338171419-9357643742086572745
ENST00000540320NBEAchr1335883729-ENST00000541481POSTNchr1338171419-8568643742085672715
ENST00000400445NBEAchr1335883729-ENST00000541179POSTNchr1338171419-9414643742086632747
ENST00000400445NBEAchr1335883729-ENST00000379749POSTNchr1338171419-9493643742087442774
ENST00000400445NBEAchr1335883729-ENST00000379747POSTNchr1338171419-9573643742088282802
ENST00000400445NBEAchr1335883729-ENST00000379743POSTNchr1338171419-9490643742087472775
ENST00000400445NBEAchr1335883729-ENST00000379742POSTNchr1338171419-9357643742086572745
ENST00000400445NBEAchr1335883729-ENST00000541481POSTNchr1338171419-8568643742085672715
ENST00000310336NBEAchr1335883729-ENST00000541179POSTNchr1338171419-908661099283352747
ENST00000310336NBEAchr1335883729-ENST00000379749POSTNchr1338171419-916561099284162774
ENST00000310336NBEAchr1335883729-ENST00000379747POSTNchr1338171419-924561099285002802
ENST00000310336NBEAchr1335883729-ENST00000379743POSTNchr1338171419-916261099284192775
ENST00000310336NBEAchr1335883729-ENST00000379742POSTNchr1338171419-902961099283292745
ENST00000310336NBEAchr1335883729-ENST00000541481POSTNchr1338171419-824061099282392716
ENST00000379939NBEAchr1335883729-ENST00000541179POSTNchr1338171419-903260554782812744
ENST00000379939NBEAchr1335883729-ENST00000379749POSTNchr1338171419-911160554783622771
ENST00000379939NBEAchr1335883729-ENST00000379747POSTNchr1338171419-919160554784462799
ENST00000379939NBEAchr1335883729-ENST00000379743POSTNchr1338171419-910860554783652772
ENST00000379939NBEAchr1335883729-ENST00000379742POSTNchr1338171419-897560554782752742
ENST00000379939NBEAchr1335883729-ENST00000541481POSTNchr1338171419-818660554781852713

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
ENST00000540320ENST00000541179NBEAchr1335883729-POSTNchr1338171419-0.0005413740.9994586
ENST00000540320ENST00000379749NBEAchr1335883729-POSTNchr1338171419-0.0004301580.99956983
ENST00000540320ENST00000379747NBEAchr1335883729-POSTNchr1338171419-0.0006855390.9993144
ENST00000540320ENST00000379743NBEAchr1335883729-POSTNchr1338171419-0.000528310.9994717
ENST00000540320ENST00000379742NBEAchr1335883729-POSTNchr1338171419-0.0004781680.99952185
ENST00000540320ENST00000541481NBEAchr1335883729-POSTNchr1338171419-0.0006766790.99932337
ENST00000400445ENST00000541179NBEAchr1335883729-POSTNchr1338171419-0.0005428060.9994572
ENST00000400445ENST00000379749NBEAchr1335883729-POSTNchr1338171419-0.0004302420.9995697
ENST00000400445ENST00000379747NBEAchr1335883729-POSTNchr1338171419-0.0006854410.99931455
ENST00000400445ENST00000379743NBEAchr1335883729-POSTNchr1338171419-0.000528820.99947125
ENST00000400445ENST00000379742NBEAchr1335883729-POSTNchr1338171419-0.0004799680.99952006
ENST00000400445ENST00000541481NBEAchr1335883729-POSTNchr1338171419-0.0006796390.9993204
ENST00000310336ENST00000541179NBEAchr1335883729-POSTNchr1338171419-0.0003247540.9996753
ENST00000310336ENST00000379749NBEAchr1335883729-POSTNchr1338171419-0.0002579890.999742
ENST00000310336ENST00000379747NBEAchr1335883729-POSTNchr1338171419-0.0004136340.9995864
ENST00000310336ENST00000379743NBEAchr1335883729-POSTNchr1338171419-0.0003235490.99967647
ENST00000310336ENST00000379742NBEAchr1335883729-POSTNchr1338171419-0.0002875350.9997124
ENST00000310336ENST00000541481NBEAchr1335883729-POSTNchr1338171419-0.0004061890.9995938
ENST00000379939ENST00000541179NBEAchr1335883729-POSTNchr1338171419-0.0003056390.99969435
ENST00000379939ENST00000379749NBEAchr1335883729-POSTNchr1338171419-0.0002424590.9997576
ENST00000379939ENST00000379747NBEAchr1335883729-POSTNchr1338171419-0.0003881360.9996119
ENST00000379939ENST00000379743NBEAchr1335883729-POSTNchr1338171419-0.0003040380.999696
ENST00000379939ENST00000379742NBEAchr1335883729-POSTNchr1338171419-0.0002705780.99972945
ENST00000379939ENST00000541481NBEAchr1335883729-POSTNchr1338171419-0.0003828710.9996171

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for NBEA-POSTN

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NBEAchr1335883729POSTNchr133817141960552002NAGLAFIELINEGSPNVCALQQILGT
NBEAchr1335883729POSTNchr133817141961092005NAGLAFIELINEGSPNVCALQQILGT
NBEAchr1335883729POSTNchr133817141964372005NAGLAFIELINEGSPNVCALQQILGT

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Potential FusionNeoAntigen Information of NBEA-POSTN in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
NBEA-POSTN_35883729_38171419.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
NBEA-POSTNchr1335883729chr13381714196109HLA-A02:21LINEGSPNV0.98780.5434817
NBEA-POSTNchr1335883729chr13381714196109HLA-A02:13LINEGSPNV0.98550.5159817
NBEA-POSTNchr1335883729chr13381714196109HLA-B45:01NEGSPNVCA0.91710.52041019
NBEA-POSTNchr1335883729chr13381714196109HLA-B41:01NEGSPNVCA0.08360.75841019
NBEA-POSTNchr1335883729chr13381714196109HLA-C01:17GSPNVCAL0.9870.95181220
NBEA-POSTNchr1335883729chr13381714196109HLA-C01:03GSPNVCAL0.98730.90631220
NBEA-POSTNchr1335883729chr13381714196109HLA-C01:02GSPNVCAL0.98720.94911220
NBEA-POSTNchr1335883729chr13381714196109HLA-A02:03LINEGSPNV0.99640.5308817
NBEA-POSTNchr1335883729chr13381714196109HLA-A02:06LINEGSPNV0.98780.5434817
NBEA-POSTNchr1335883729chr13381714196109HLA-A69:01LINEGSPNV0.89930.5925817

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Potential FusionNeoAntigen Information of NBEA-POSTN in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
NBEA-POSTN_35883729_38171419.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
NBEA-POSTNchr1335883729chr13381714196109DRB1-0419GLAFIELINEGSPNV217
NBEA-POSTNchr1335883729chr13381714196109DRB1-0419AGLAFIELINEGSPN116
NBEA-POSTNchr1335883729chr13381714196109DRB1-0443GLAFIELINEGSPNV217
NBEA-POSTNchr1335883729chr13381714196109DRB1-0443AGLAFIELINEGSPN116
NBEA-POSTNchr1335883729chr13381714196109DRB1-0461GLAFIELINEGSPNV217
NBEA-POSTNchr1335883729chr13381714196109DRB1-0461AGLAFIELINEGSPN116

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Fusion breakpoint peptide structures of NBEA-POSTN

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
3649IELINEGSPNVCALNBEAPOSTNchr1335883729chr13381714196109

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NBEA-POSTN

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B53:011A1O3649IELINEGSPNVCAL-2.69901-2.81241
HLA-B53:011A1O3649IELINEGSPNVCAL-1.64072-2.67602
HLA-B51:011E283649IELINEGSPNVCAL-3.89938-4.01278
HLA-B51:011E283649IELINEGSPNVCAL-3.06372-4.09902
HLA-B57:032BVO3649IELINEGSPNVCAL-3.85739-3.97079
HLA-B57:032BVO3649IELINEGSPNVCAL-2.16065-3.19595
HLA-A03:012XPG3649IELINEGSPNVCAL-3.98424-4.09764
HLA-A03:012XPG3649IELINEGSPNVCAL-3.8004-4.8357
HLA-B14:023BVN3649IELINEGSPNVCAL-5.50909-5.62249
HLA-B14:023BVN3649IELINEGSPNVCAL-3.39692-4.43222
HLA-B52:013W393649IELINEGSPNVCAL-4.60651-4.71991
HLA-B52:013W393649IELINEGSPNVCAL-3.34519-4.38049
HLA-B18:014JQV3649IELINEGSPNVCAL-4.4543-4.5677
HLA-B18:014JQV3649IELINEGSPNVCAL-3.52041-4.55571
HLA-A11:014UQ23649IELINEGSPNVCAL-8.57217-8.68557
HLA-A11:014UQ23649IELINEGSPNVCAL-5.25237-6.28767
HLA-A24:025HGA3649IELINEGSPNVCAL-5.46268-5.57608
HLA-A24:025HGA3649IELINEGSPNVCAL-4.17359-5.20889
HLA-B57:015VUD3649IELINEGSPNVCAL-3.01236-3.12576
HLA-B57:015VUD3649IELINEGSPNVCAL-2.64732-3.68262
HLA-C08:026JTP3649IELINEGSPNVCAL-5.68918-5.80258
HLA-C08:026JTP3649IELINEGSPNVCAL-2.35623-3.39153
HLA-B37:016MT43649IELINEGSPNVCAL-1.0889-2.1242
HLA-B27:056PYJ3649IELINEGSPNVCAL-3.72452-3.83792
HLA-B27:056PYJ3649IELINEGSPNVCAL-2.83784-3.87314
HLA-B27:036PZ53649IELINEGSPNVCAL-3.01578-3.12918
HLA-B27:036PZ53649IELINEGSPNVCAL-0.24885-1.28415
HLA-B44:053DX83649IELINEGSPNVCAL-4.88127-4.99467
HLA-B44:053DX83649IELINEGSPNVCAL-3.81413-4.84943
HLA-B44:021M6O3649IELINEGSPNVCAL-2.54607-3.58137
HLA-B44:021M6O3649IELINEGSPNVCAL-2.05297-2.16637
HLA-B07:025EO03649IELINEGSPNVCAL-0.497899-1.5332
HLA-A02:016TDR3649IELINEGSPNVCAL-1.85788-2.89318
HLA-A02:016TDR3649IELINEGSPNVCAL-2.64204-2.75544

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Vaccine Design for the FusionNeoAntigens of NBEA-POSTN

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
NBEA-POSTNchr1335883729chr13381714191019NEGSPNVCATGAAGGAAGCCCAAATGTCTGTGCCCT
NBEA-POSTNchr1335883729chr13381714191220GSPNVCALAAGCCCAAATGTCTGTGCCCTTCA
NBEA-POSTNchr1335883729chr1338171419817LINEGSPNVCATCAATGAAGGAAGCCCAAATGTCTG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
NBEA-POSTNchr1335883729chr1338171419116AGLAFIELINEGSPNAGGACTTGCATTTATTGAGCTCATCAATGAAGGAAGCCCAAATGT
NBEA-POSTNchr1335883729chr1338171419217GLAFIELINEGSPNVACTTGCATTTATTGAGCTCATCAATGAAGGAAGCCCAAATGTCTG

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Information of the samples that have these potential fusion neoantigens of NBEA-POSTN

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample
PRADNBEA-POSTNchr1335883729ENST00000310336chr1338171419ENST00000379742TCGA-CH-5753-01A

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Potential target of CAR-T therapy development for NBEA-POSTN

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to NBEA-POSTN

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to NBEA-POSTN

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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