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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene Breakpoints

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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Geness

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Fusion Genomic Features

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Fusion Gene ORF Annotations

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Fusion Protein Retained/Non-Retained Functional Features

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Fusion Transcript Sequences

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Fusion Protein Sequences

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Personalized Fusion Protein Sequences

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Fusion Gene Expressed Samples

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Related Drugs

Fusion gene:BRD4_PGLYRP2 (FusionGDB2 ID:HG23476TG114770)

Fusion Gene Summary for BRD4_PGLYRP2

check button Fusion gene summary
Fusion gene informationFusion gene name: BRD4_PGLYRP2
Fusion gene ID: hg23476tg114770
HgeneTgene
Gene symbol

BRD4

PGLYRP2

Gene ID

23476

114770

Gene namebromodomain containing 4peptidoglycan recognition protein 2
SynonymsCAP|CDLS6|FSHRG4|HUNK1|HUNKI|MCAPHMFT0141|PGLYRPL|PGRP-L|PGRPL|TAGL-like|tagL|tagL-alpha|tagl-beta
Cytomap

19p13.12

19p13.12

Type of geneprotein-codingprotein-coding
Descriptionbromodomain-containing protein 4chromosome-associated proteinfemale sterile homeotic related gene 4mitotic chromosome-associated proteinN-acetylmuramoyl-L-alanine amidasepeptidoglycan recognition protein Lpeptidoglycan recognition protein long
Modification date2024041620240305
UniProtAcc

O60885

.
Ensembl transtripts involved in fusion geneENST00000360016, ENST00000263377, 
ENST00000371835, ENST00000602230, 
Fusion gene scores* DoF score* DoF score (Degree of Frequency) = # partners X # break points X # disease types
45 X 81 X 27=98415
* DoF score (Degree of Frequency) = # partners X # break points X # disease types
1 X 6 X 2=12
# samples 1177
** MAII score** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)
log2(117/98415*10)=-6.394297786907
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)
log2(7/12*10)=2.54432051622381
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: BRD4 [Title/Abstract] AND PGLYRP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBRD4(15443100)-PGLYRP2(15580740), # samples:1


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Fusion Gene Breakpoints for BRD4_PGLYRP2


check button RNA-seq based exon junction arranged fusion gene breakpoints from 8 resources (TCGA, CCLE, cBioPortal, GenBank, ChimerDB, ChimerKB, ChildHoodFusions, and GTEx). For the expressed sample information, go to Fusion Gene Sample section.
HgeneHchrHbpTgeneTchrTbp
BRD4chr1915443100PGLYRP2chr1915580740
BRD4chr1915443101PGLYRP2chr1915580740
BRD4chr1915383681PGLYRP2chr1915587576
BRD4chr1915332290PGLYRP2chr1915469929


check button DNA-seq based exon junction arranged fusion gene breakpoints from dbVar. For the expressed sample information, go to Fusion Gene Sample section.
HgeneHchrHbpTgeneTchrTbpSV type
BRD4chr1915403050PGLYRP2chr1915586364DEL
BRD4chr1915425752PGLYRP2chr1915587185DEL


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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Genes for BRD4_PGLYRP2


check button To generate these tumorigenic scenario annotations, we implemented a deduction-first, retrieval-later computational framework. The pipeline first applies rule-guided reasoning across ten core mechanistic categories (M1–M10) derived from fusion gene biology to infer candidate mechanisms, tumorigenic scenarios, targeting points, and targeting backgrounds. To ensure empirical accountability, a governed Python workflow retrieves literature candidates via NCBI E-utilities and Europe PMC using tiered searches. Using JSON Schema-constrained LLM evidence judges (GPT-5.6 Luna and Terra), retrieved articles are evaluated for specificity and confidence without de novo PMID generation. This produces two distinct versions: a strict version restricted to high- or medium-confidence fusion-specific evidence, and an extended version incorporating broader gene-, pathway-, and contextual evidence.
* We have 10 tumorigenic mechanism categories of fusion genes as shown below.
Constitutively Active Kinases, Catalytic Domain Dysregulation, & Transmembrane Ligand FusionsAberrant Chimeric Transcription Factor / Fusion Transcription Factor ActivityEpigenetic Reprogramming / Histone Modifier DysregulationChromatin Remodeling DysregulationCondensate-Driven Transcriptional Rewiring / LLPPromoter / Enhancer HijackingDominant-Negative AntagonismCell Cycle / Checkpoint Bypass / RNA Processing DysregulationSubcellular Mislocalization / Spatial DysregulationNuclear Body / Sub-organellar Architecture Disruption & Differentiation Blockade

* Strict version: Restricted to high- or medium-confidence fusion-specific evidence.
Fusion Gene NameMechanism CategoryMechanism PubMedTumorigenic ScenariosTumorigenic Scenario PubMedTargeting PointsTargeting PubMedMechanism BackgroundMechanism Background PubMed
BRD4-PGLYRP2
Epigenetic Reprogramming / Histone Modifier Dysregulation
M3
Promoter swap drives elevated PGLYRP2 expression, modifying extracellular matrix interactions and innate immune sensing.BET inhibitors; standard chemotherapySolid tumors

* Extended version: Includes all strict-level fusion evidence plus broader gene-, pathway-, and low-confidence contextual evidence.
Fusion Gene NameMechanism CategoryMechanism PubMedTumorigenic ScenariosTumorigenic Scenario PubMedTargeting PointsTargeting PubMedMechanism BackgroundMechanism Background PubMed
BRD4-PGLYRP2
Epigenetic Reprogramming / Histone Modifier Dysregulation
M3
Promoter swap drives elevated PGLYRP2 expression, modifying extracellular matrix interactions and innate immune sensing.Evidence level: Limited indirect gene evidence; Confidence: Low; PMID: 31479523; Title: Tumor-Derived Peptidoglycan Recognition Protein 2 Predicts Survival and Antitumor Immune Responses in Hepatocellular Carcinoma.BET inhibitors; standard chemotherapySolid tumorsEvidence level: Limited indirect gene evidence; Confidence: Low; PMID: 31479523; Title: Tumor-Derived Peptidoglycan Recognition Protein 2 Predicts Survival and Antitumor Immune Responses in Hepatocellular Carcinoma.; PMID: 18649358; Title: Replication of a genome-wide case-control study of esophageal squamous cell carcinoma.

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BRD4

O60885

.

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneBRD4

GO:0032968

positive regulation of transcription elongation by RNA polymerase II

19103749

HgeneBRD4

GO:0043123

positive regulation of canonical NF-kappaB signal transduction

19103749

HgeneBRD4

GO:0045944

positive regulation of transcription by RNA polymerase II

23086925|23317504|24360279

HgeneBRD4

GO:0050727

regulation of inflammatory response

19103749

TgenePGLYRP2

GO:0016045

detection of bacterium

11461926

TgenePGLYRP2

GO:0050830

defense response to Gram-positive bacterium

11461926


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Fusion Genomic Features for BRD4_PGLYRP2


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) of In-frame fusion genes. 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)
BRD4chr1915443100-PGLYRP2chr1915580740-4.44e-151.00e+00


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) of 5UTR-3CSD fusion genes (N-truncated cases).
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
BRD4chr1915443100-PGLYRP2chr1915580740-4.44e-151.00e+00

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) of 5CDS-3UTR fusion genes (C-truncated cases).
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of six genomic regulatory feature tracks across a ±5 kb window centered on the fusion breakpoints. We input the breakpoint sequences into AlphaGenome and obtained predicted genome tracks at single-base-pair resolution for each modality by running a single forward pass over the reference sequence. Specifically, for each breakpoint, AlphaGenome processed and returned predicted track data across diverse modalities, which were then averaged across all tracks within each output type and visualized across the ±5 kb window. The left panel shows the 5'-gene breakpoint ±5 kb area, and the right panel shows the 3'-gene breakpoint area, with tracks grouped by category: chromatin accessibility (DNase-seq, ATAC-seq), active transcription (RNA-seq, CAGE), and chromatin binding (ChIP-Histone, ChIP-TF).
genomic feature

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Fusion Gene ORF Annotations for BRD4_PGLYRP2

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-3CDSENST00000360016ENST00000292609BRD4chr19

15443100

-PGLYRP2chr19

15580740

-
5UTR-3CDSENST00000360016ENST00000340880BRD4chr19

15443100

-PGLYRP2chr19

15580740

-

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the In-frame Fusion Genes.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)
Seq length
(peptide)

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the 5UTR-3CDS Fusion Genes for N-Truncated Protein Search.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)
Seq length
(peptide)
ENST00000360016ENST00000292609BRD4chr1915443100PGLYRP2chr19155807400739
ENST00000360016ENST00000340880BRD4chr1915443100PGLYRP2chr19155807400277

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the 5CDS-3UTR Fusion Genes for C-Truncated Protein Search.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)
Seq length
(peptide)

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.
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score

check buttonDeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5UTR-3CDS Fusion Genes (Potential N-Truncated Proteins).
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score
ENST00000360016ENST00000292609BRD4chr1915443100PGLYRP2chr19155807400.00e+002.09e-01
ENST00000360016ENST00000340880BRD4chr1915443100PGLYRP2chr19155807400.00e+008.59e-02

check buttonDeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5CDS-3UTR Fusion Genes (Potential C-Truncated Proteins).
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score

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Fusion Protein Retained/Non-Retained Functional Features for BRD4_PGLYRP2

check buttonProtein Level Annotation from FGviewer
* Retention 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.
fgviewer annotation
- In-frame and retained protein feature among the 13 regional features (visualization across fusion protein length).
No matching images found for ${hg}_${tg}.

- In-frame and retained protein feature among the 13 regional features (texts).
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


check button - Retained PPIs in in-frame fusion.
PartnerHgeneHbpTgeneTbpENSTUniProtStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerHgeneHbpTgeneTbpENSTUniProtStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Fusion Transcript Sequence for BRD4_PGLYRP2

check button In-frame Fusion Transcript Sequences.

check button N-Truncated Transcript (5UTR-3CDS) Sequences
>BRD4_PGLYRP2_ENST00000360016_ENST00000292609_15443100_15580740 length=1285nt
Breakpoint=0nt
TTTCGTGGTGGGCTCGGACGGCTACGTGTACGAGGGACGCGGCTGGCACTGGGTGGGCGCCCACACGCTCGGCCACAACTCCCGGGGCTTCGGCGTGGCCATAGTGGGCAACTACACCGCGGCGCTGCCCACCGAGGCCGCTCTGCGCAC
GGTGCGCGACACGCTCCCGAGTTGTGCGGTGCGCGCCGGCCTCCTGCGGCCAGACTACGCGCTGCTGGGCCACCGCCAGCTGGTGCGCACCGACTGCCCCGGCGACGCGCTCTTCGACCTGCTGCGCACCTGGCCGCACTTCACCGCGGT
GAGTCTTCGCAGCCTGCACTACACGGCCCGCCGCCCCTCCGTCTACACAAGCTCCACGAGGCCCCTGCCCCCTGCCTGTAACAGCTGTGCCCGCACAGCCTCAGCCAGGCCCCCAACTTCCCGGCGGCACGTCTATTCAGGAAACCTAGG
CCCAGCCTTTGCGGGTCACTCTGCGGGCAACATCCCTGATCCTGTGACTTCTGCCTATGCAGCCTCAGCTCAGCCCCAGACCCAGCCAGCCTGTCCTTTCCCCAGCTCCTAATACCTCTACCTTTCCAGCCAAGGCATGGACCCTGACAC
CTGCCAACAGCCCCTCTGCCCTCACAACCTCAGCCTGGCCTTCATGACTTCTCTACCCAAGTCACAACCTGTCAGGCTGCACCACCTCATCCTGGCCCGCCGAACCTTGACCTCACCCCTGCCCCTACCCGAAGGCCCTCTGTCCACACA
ACATGAACCTAGGCTGTGACCTTTTGCCTTCACAACCTCTGTCCAGTCCTTAATCCTGTGTTGCAATTCTCTGTCCAGACAATCTCAACTCTGAGGTTGCTTGTTTCGTCCCTGACTCCTTAACCCCTGATGACAACTCTTATGCCAGCA
CAACTTTGACCTGATGACCTCATCCCAGCCCTTGATCGCCATCACTAAAACAATTTTAGAATCACACCTGGACAATCTCGTGCTACCTACATACTGCCACTCCATTTCATTAAGCTATTGACTAGCACATCCATCTCGGCCTATAGTTGG
CTTTGTCCTCACTCTCTCACTTTGGGCCACTGTCCCCTCCCTGATCCAGGGTTCCACCACCAGGAGGGCAGACCCAGCCACATACCACAACCACCCCCAAGCCTCACACTCCCTTGTCTTTTTCCAGACTGTTAAGCCAAGACCTGCCAG
GAGTGTCTCTAAGAGATCCAGGAGGGAGCCACCCCCAAGGACCCTGCCAGCCACAGACCTCCAATAAAGACAGCATGGAAACAAA

>BRD4_PGLYRP2_ENST00000360016_ENST00000340880_15443100_15580740 length=406nt
Breakpoint=0nt
TTTCGTGGTGGGCTCGGACGGCTACGTGTACGAGGGACGCGGCTGGCACTGGGTGGGCGCCCACACGCTCGGCCACAACTCCCGGGGCTTCGGCGTGGCCATAGTGGGCAACTACACCGCGGCGCTGCCCACCGAGGCCGCTCTGCGCAC
GGTGCGCGACACGCTCCCGAGTTGTGCGGTGCGCGCCGGCCTCCTGCGGCCAGACTACGCGCTGCTGGGCCACCGCCAGCTGGTGCGCACCGACTGCCCCGGCGACGCGCTCTTCGACCTGCTGCGCACCTGGCCGCACTTCACCGCGAC
TGTTAAGCCAAGACCTGCCAGGAGTGTCTCTAAGAGATCCAGGAGGGAGCCACCCCCAAGGACCCTGCCAGCCACAGACCTCCAATAAAGACAGCATGGAAACAAA


check button C-Truncated Transcript (5CDS-3UTR) Sequences

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Fusion Protein Sequence for BRD4_PGLYRP2

check button In-frame Fusion Protein Sequences.

check button N-Truncated Protein (5UTR-3CDS) Sequences
>BRD4_PGLYRP2_ENST00000360016_ENST00000292609_15443100_15580740 length=739nt
MLEIDNRLCLQSPENDHCFPDAQSAADYLGALSAVERLDFPYPLRDVRGEPLEPPEPSVPLLPLLVAGAVLLLVILVLGVMVARRKREHSTLWFPEGFSLHKDVASGHKGRREPVGQDALGMKNMAKGESLMGEVATDWMDTECPEAKRL
KVEEPGMGAEEAVDCRQWTQHHLVAADIRVAPAMALTPPQGDADADGMDVNVRGPDGFTPLMLASFCGGALEPMPTEEDEADDTSASIISDLICQGAQLGARTDRTGETALHLAARYARADAAKRLLDAGADTNAQDHSGRTPLHTAVTA
DAQGVFQILIRNRSTDLDARMADGSTALILAARLAVEGMVEELIASHADVNAVDELGKSALHWAAAVNNVEATLALLKNGANKDMQDSKEETPLFLAAREGSYEAAKLLLDHFANREITDHLDRLPRDVAQERLHQDIVRLLDQPSGPRS
PPGPHGLGPLLCPPGAFLPGLKAAQSGSKKSRRPPGKAGLGPQGPRGRGKKLTLACPGPLADSSVTLSPVDSLDSPRPFGGPPASPGGFPLEGPYAAATATAVSLAQLGGPGRAGLGRQPPGGCVLSLGLLNPVAVPLDWARLPPPAPPG
PSFLLPLAPGPQLLNPGTPVSPQERPPPYLAVPGHGEEYPAAGAHSSPPKARFLRVPSEHPYLTPSPESPEHWASPSPPSLSDWSESTPSPATATGAMATTTGALPAQPLPLSVPSSLAQAQTQLGPQPEVTPKRQVLA

>BRD4_PGLYRP2_ENST00000360016_ENST00000340880_15443100_15580740 length=277nt
MDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGWFWVCPGGGDICMYRHALPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKADFKAGKALVISGREVFEFRP
ELVNDDDEEADDTRYTQGTGGDEVDDSVSVNDIDLSLYIPRDVDETGITVASLERFSTYTSDKDENKLSEASGGRAENGERSDLEEDNEREGTENGAIDAVPVDENLFTGEDLDELEEELNTLDLEE


check button C-Truncated Protein (5CDS-3UTR) Sequences

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Personalized Fusion Protein Sequence for BRD4_PGLYRP2


check button TCGA Kinase/DNA-binding Domain Mutated Fusion Protein Sequences
NumGene GroupDomain LociFusion Protein IDFusion Gene NamePartnerMutated Residue in WT ProteinSeq. LengthMutated Residue in Fusion Protein

check button CCLE Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

NumGene GroupDomain LociFusion Protein IDFusion Gene NamePartnerMutated Residue in WT ProteinSeq. LengthMutated Residue in Fusion Protein

check button TCGA All Mutated Fusion Protein Sequences


Fusion Protein IDSample IDMutated PartnerAAchange in WTSeq. LengthAAchange in Fusion

check button CCLE All Mutated Fusion Protein Sequences


Fusion Protein IDSample IDMutated PartnerAAchange in WTSeq. LengthAAchange in Fusion

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Fusion Gene Exprssed Samples for BRD4_PGLYRP2


check buttonRNA-seq based fusion gene expressed samples.
SourceStudyDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDBBLCATCGA-UY-A78K-01ABRD4

chr19

15443100-PGLYRP2

chr19

15580740

-
WashUBLCATCGA-UY-A78K-01ABRD4

chr19

15443101-PGLYRP2

chr19

15580740

-
cBioPortalMSK_IMPACT_50K_2026MIXEDP-0015507-T01-IM6BRD4

chr19

15383681PGLYRP2

chr19

15587576

cBioPortalMSK_MET_2021MIXEDP-0015507-T01-IM6BRD4

chr19

15383681PGLYRP2

chr19

15587576

cBioPortalBLCA_TCGA_PAN_CAN_ATLAS_2018BLCATCGA-UY-A78K-01BRD4

chr19

15332290PGLYRP2

chr19

15469929


check buttonDNA-seq based fusion gene expressed samples.
SourceStudyDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrandSV type
dbVarnstd68Unknown_CellBRD4

chr19

15403050PGLYRP2

chr19

15586364

DEL
dbVarnstd71Unknown_CellSP54956BRD4

chr19

15425752PGLYRP2

chr19

15587185

DEL


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Related Drugs for BRD4_PGLYRP2


check button PubMed Abstract Search With ['A-B' AND 'drug'], ['A::B' AND 'drug']
* For more details on the Studied, Reported, Approved Drugs targeting this fusion gene, Go to FusionPub.
PMIDFusion Gene NameDrugStudy Title

check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status