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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:BPTF-NOL11

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: BPTF-NOL11
FusionPDB ID: 10092
FusionGDB2.0 ID: 10092
HgeneTgene
Gene symbol

BPTF

NOL11

Gene ID

2186

25926

Gene namebromodomain PHD finger transcription factornucleolar protein 11
SynonymsFAC1|FALZ|NEDDFL|NURF301-
Cytomap

17q24.2

17q24.2

Type of geneprotein-codingprotein-coding
Descriptionnucleosome-remodeling factor subunit BPTFbromodomain and PHD domain transcription factorbromodomain and PHD finger-containing transcription factorfetal Alz-50 clone 1 proteinfetal Alz-50 reactive clone 1fetal Alzheimer antigennucleosome remodeling fnucleolar protein 11
Modification date2020031320200313
UniProtAcc

Q12830

Main function of 5'-partner protein: FUNCTION: Histone-binding component of NURF (nucleosome-remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. May also regulate transcription through direct binding to DNA or transcription factors.

Q9H8H0

Main function of 5'-partner protein: FUNCTION: Ribosome biogenesis factor. May be required for both optimal rDNA transcription and small subunit (SSU) pre-rRNA processing at sites A', A0, 1 and 2b. {ECO:0000269|PubMed:22916032}.
Ensembl transtripts involved in fusion geneENST idsENST00000306378, ENST00000321892, 
ENST00000335221, ENST00000424123, 
ENST00000577770, 
ENST00000581966, 
ENST00000535137, ENST00000253247, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score27 X 21 X 13=73713 X 9 X 6=162
# samples 429
** MAII scorelog2(42/7371*10)=-4.1333991254172
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/162*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: BPTF [Title/Abstract] AND NOL11 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: BPTF [Title/Abstract] AND NOL11 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BPTF(65944422)-NOL11(65715790), # samples:3
BPTF(65862803)-NOL11(65739859), # samples:3
Anticipated loss of major functional domain due to fusion event.BPTF-NOL11 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.
BPTF-NOL11 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.
BPTF-NOL11 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.
BPTF-NOL11 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.
BPTF-NOL11 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
BPTF-NOL11 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
BPTF-NOL11 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
BPTF-NOL11 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
BPTF-NOL11 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneBPTF

GO:0000122

negative regulation of transcription by RNA polymerase II

10727212

HgeneBPTF

GO:0006338

chromatin remodeling

14609955



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/chr17:65944422/chr17:65715790)
- 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 BPTF (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 NOL11 (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)
ENST00000335221BPTFchr1765944422+ENST00000253247NOL11chr1765715790+1062779366199543297
ENST00000321892BPTFchr1765944422+ENST00000253247NOL11chr1765715790+11056836561103833440
ENST00000306378BPTFchr1765944422+ENST00000253247NOL11chr1765715790+10677798660100043314
ENST00000424123BPTFchr1765944422+ENST00000253247NOL11chr1765715790+101497458094763158

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
ENST00000335221ENST00000253247BPTFchr1765944422+NOL11chr1765715790+0.0005258240.9994742
ENST00000321892ENST00000253247BPTFchr1765944422+NOL11chr1765715790+0.0003845070.99961543
ENST00000306378ENST00000253247BPTFchr1765944422+NOL11chr1765715790+0.0003554670.9996445
ENST00000424123ENST00000253247BPTFchr1765944422+NOL11chr1765715790+0.0004959410.9995041

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 BPTF-NOL11

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
BPTFchr1765944422NOL11chr176571579074582486RALLDKDLQIEVQVSDQKPLGSWSVK
BPTFchr1765944422NOL11chr176571579079362625RALLDKDLQIEVQVSDQKPLGSWSVK
BPTFchr1765944422NOL11chr176571579079862642RALLDKDLQIEVQVSDQKPLGSWSVK
BPTFchr1765944422NOL11chr176571579083652768RALLDKDLQIEVQVSDQKPLGSWSVK

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Potential FusionNeoAntigen Information of BPTF-NOL11 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.
BPTF-NOL11_65944422_65715790.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)
BPTF-NOL11chr1765944422chr17657157907986HLA-B13:02KDLQIEVQV0.96030.9848514
BPTF-NOL11chr1765944422chr17657157907986HLA-B37:01KDLQIEVQV0.92020.6199514
BPTF-NOL11chr1765944422chr17657157907986HLA-B39:13VQVSDQKPL0.57110.85351120
BPTF-NOL11chr1765944422chr17657157907986HLA-B15:03VQVSDQKPL0.46120.68681120
BPTF-NOL11chr1765944422chr17657157907986HLA-B13:01VQVSDQKPL0.42650.90871120
BPTF-NOL11chr1765944422chr17657157907986HLA-B57:01QVSDQKPLGSW0.99990.89131223
BPTF-NOL11chr1765944422chr17657157907986HLA-B58:01QVSDQKPLGSW0.99920.86511223
BPTF-NOL11chr1765944422chr17657157907986HLA-A32:13QVSDQKPLGSW0.9750.91611223
BPTF-NOL11chr1765944422chr17657157907986HLA-B40:40KDLQIEVQV0.99550.7224514
BPTF-NOL11chr1765944422chr17657157907986HLA-B15:73VQVSDQKPL0.88680.87361120
BPTF-NOL11chr1765944422chr17657157907986HLA-B15:30VQVSDQKPL0.8050.79821120
BPTF-NOL11chr1765944422chr17657157907986HLA-B39:02VQVSDQKPL0.73130.85661120
BPTF-NOL11chr1765944422chr17657157907986HLA-B57:10QVSDQKPLGSW0.99990.89131223
BPTF-NOL11chr1765944422chr17657157907986HLA-B57:04QVSDQKPLGSW0.99980.64311223
BPTF-NOL11chr1765944422chr17657157907986HLA-B57:02QVSDQKPLGSW0.99950.93661223
BPTF-NOL11chr1765944422chr17657157907986HLA-A25:01QVSDQKPLGSW0.96230.85571223

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Potential FusionNeoAntigen Information of BPTF-NOL11 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.
BPTF-NOL11_65944422_65715790.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)
BPTF-NOL11chr1765944422chr17657157907986DRB1-0906LQIEVQVSDQKPLGS722
BPTF-NOL11chr1765944422chr17657157907986DRB1-0906QIEVQVSDQKPLGSW823
BPTF-NOL11chr1765944422chr17657157907986DRB1-0906DLQIEVQVSDQKPLG621
BPTF-NOL11chr1765944422chr17657157907986DRB1-1439LQIEVQVSDQKPLGS722
BPTF-NOL11chr1765944422chr17657157907986DRB4-0101DLQIEVQVSDQKPLG621
BPTF-NOL11chr1765944422chr17657157907986DRB4-0101KDLQIEVQVSDQKPL520
BPTF-NOL11chr1765944422chr17657157907986DRB4-0103DLQIEVQVSDQKPLG621
BPTF-NOL11chr1765944422chr17657157907986DRB4-0103KDLQIEVQVSDQKPL520
BPTF-NOL11chr1765944422chr17657157907986DRB4-0104DLQIEVQVSDQKPLG621
BPTF-NOL11chr1765944422chr17657157907986DRB4-0104KDLQIEVQVSDQKPL520
BPTF-NOL11chr1765944422chr17657157907986DRB4-0104DKDLQIEVQVSDQKP419
BPTF-NOL11chr1765944422chr17657157907986DRB4-0106DLQIEVQVSDQKPLG621
BPTF-NOL11chr1765944422chr17657157907986DRB4-0106KDLQIEVQVSDQKPL520
BPTF-NOL11chr1765944422chr17657157907986DRB4-0107DLQIEVQVSDQKPLG621
BPTF-NOL11chr1765944422chr17657157907986DRB4-0107KDLQIEVQVSDQKPL520
BPTF-NOL11chr1765944422chr17657157907986DRB4-0108DLQIEVQVSDQKPLG621
BPTF-NOL11chr1765944422chr17657157907986DRB4-0108KDLQIEVQVSDQKPL520

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Fusion breakpoint peptide structures of BPTF-NOL11

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
1243DLQIEVQVSDQKPLBPTFNOL11chr1765944422chr17657157907986

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BPTF-NOL11

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-B14:023BVN1243DLQIEVQVSDQKPL-7.9962-8.1096
HLA-B14:023BVN1243DLQIEVQVSDQKPL-5.70842-6.74372
HLA-B52:013W391243DLQIEVQVSDQKPL-6.83737-6.95077
HLA-B52:013W391243DLQIEVQVSDQKPL-4.4836-5.5189
HLA-A11:014UQ21243DLQIEVQVSDQKPL-10.0067-10.1201
HLA-A11:014UQ21243DLQIEVQVSDQKPL-9.03915-10.0745
HLA-A24:025HGA1243DLQIEVQVSDQKPL-6.56204-6.67544
HLA-A24:025HGA1243DLQIEVQVSDQKPL-5.42271-6.45801
HLA-B44:053DX81243DLQIEVQVSDQKPL-7.85648-8.89178
HLA-B44:053DX81243DLQIEVQVSDQKPL-5.3978-5.5112
HLA-A02:016TDR1243DLQIEVQVSDQKPL-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of BPTF-NOL11

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
BPTF-NOL11chr1765944422chr17657157901120VQVSDQKPLGTGCAGGTTTCTGATCAGAAACCCTTG
BPTF-NOL11chr1765944422chr17657157901223QVSDQKPLGSWCAGGTTTCTGATCAGAAACCCTTGGGGAGCTGG
BPTF-NOL11chr1765944422chr1765715790514KDLQIEVQVAAGGATCTGCAAATTGAAGTGCAGGTT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
BPTF-NOL11chr1765944422chr1765715790419DKDLQIEVQVSDQKPGACAAGGATCTGCAAATTGAAGTGCAGGTTTCTGATCAGAAACCC
BPTF-NOL11chr1765944422chr1765715790520KDLQIEVQVSDQKPLAAGGATCTGCAAATTGAAGTGCAGGTTTCTGATCAGAAACCCTTG
BPTF-NOL11chr1765944422chr1765715790621DLQIEVQVSDQKPLGGATCTGCAAATTGAAGTGCAGGTTTCTGATCAGAAACCCTTGGGG
BPTF-NOL11chr1765944422chr1765715790722LQIEVQVSDQKPLGSCTGCAAATTGAAGTGCAGGTTTCTGATCAGAAACCCTTGGGGAGC
BPTF-NOL11chr1765944422chr1765715790823QIEVQVSDQKPLGSWCAAATTGAAGTGCAGGTTTCTGATCAGAAACCCTTGGGGAGCTGG

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Information of the samples that have these potential fusion neoantigens of BPTF-NOL11

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
TGCTBPTF-NOL11chr1765944422ENST00000306378chr1765715790ENST00000253247TCGA-2G-AAKL-01A

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Potential target of CAR-T therapy development for BPTF-NOL11

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 BPTF-NOL11

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 BPTF-NOL11

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