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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:BMP4-LRR1 (FusionGDB2 ID:9868)

Fusion Gene Summary for BMP4-LRR1

check button Fusion gene summary
Fusion gene informationFusion gene name: BMP4-LRR1
Fusion gene ID: 9868
HgeneTgene
Gene symbol

BMP4

LRR1

Gene ID

652

122769

Gene namebone morphogenetic protein 4leucine rich repeat protein 1
SynonymsBMP2B|BMP2B1|MCOPS6|OFC11|ZYME4-1BBLRR|LRR-1|PPIL5
Cytomap

14q22.2

14q21.3

Type of geneprotein-codingprotein-coding
Descriptionbone morphogenetic protein 4bone morphogenetic protein 2Bleucine-rich repeat protein 14-1BB-mediated signaling moleculeLRR-repeat protein 1cyclophilin-like 5epididymis secretory sperm binding proteinpeptidylprolyl isomerase (cyclophilin)-like 5peptidylprolyl isomerase-like 5
Modification date2020032920200313
UniProtAcc

P12644

Q96L50

Ensembl transtripts involved in fusion geneENST00000245451, ENST00000558489, 
ENST00000417573, ENST00000558984, 
ENST00000559087, 		ENST00000298288, 
ENST00000318317, ENST00000557531, 
Fusion gene scores* DoF score2 X 2 X 2=84 X 3 X 2=24
# samples 24
** MAII scorelog2(2/8*10)=1.32192809488736log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: BMP4 [Title/Abstract] AND LRR1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBMP4(54423268)-LRR1(50069088), # 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
HgeneBMP4

GO:0000122

negative regulation of transcription by RNA polymerase II

9187146

HgeneBMP4

GO:0000186

activation of MAPKK activity

17600318|17992660

HgeneBMP4

GO:0001649

osteoblast differentiation

17720811

HgeneBMP4

GO:0001657

ureteric bud development

12141440

HgeneBMP4

GO:0001658

branching involved in ureteric bud morphogenesis

12631064

HgeneBMP4

GO:0001934

positive regulation of protein phosphorylation

14749725

HgeneBMP4

GO:0001938

positive regulation of endothelial cell proliferation

17992660

HgeneBMP4

GO:0002043

blood vessel endothelial cell proliferation involved in sprouting angiogenesis

18787191

HgeneBMP4

GO:0002244

hematopoietic progenitor cell differentiation

15451575

HgeneBMP4

GO:0003323

type B pancreatic cell development

11865031

HgeneBMP4

GO:0003337

mesenchymal to epithelial transition involved in metanephros morphogenesis

10706139

HgeneBMP4

GO:0007182

common-partner SMAD protein phosphorylation

20573232

HgeneBMP4

GO:0008284

positive regulation of cell proliferation

15516325

HgeneBMP4

GO:0008285

negative regulation of cell proliferation

9187146

HgeneBMP4

GO:0009791

post-embryonic development

8674409

HgeneBMP4

GO:0010453

regulation of cell fate commitment

18823971

HgeneBMP4

GO:0010595

positive regulation of endothelial cell migration

17992660

HgeneBMP4

GO:0010628

positive regulation of gene expression

24906886|28124060

HgeneBMP4

GO:0010629

negative regulation of gene expression

28124060

HgeneBMP4

GO:0010862

positive regulation of pathway-restricted SMAD protein phosphorylation

9389648|16816361|17244894|20559569

HgeneBMP4

GO:0010942

positive regulation of cell death

8674409

HgeneBMP4

GO:0021537

telencephalon development

9187146

HgeneBMP4

GO:0030224

monocyte differentiation

21149635

HgeneBMP4

GO:0030225

macrophage differentiation

21149635

HgeneBMP4

GO:0030501

positive regulation of bone mineralization

14749725|18436533

HgeneBMP4

GO:0030509

BMP signaling pathway

9389648|18436533

HgeneBMP4

GO:0032092

positive regulation of protein binding

23610558

HgeneBMP4

GO:0032967

positive regulation of collagen biosynthetic process

17720811

HgeneBMP4

GO:0034504

protein localization to nucleus

17244894

HgeneBMP4

GO:0042306

regulation of protein import into nucleus

22529382

HgeneBMP4

GO:0042326

negative regulation of phosphorylation

17244894

HgeneBMP4

GO:0043065

positive regulation of apoptotic process

9187146|10706139

HgeneBMP4

GO:0043066

negative regulation of apoptotic process

17992660

HgeneBMP4

GO:0043407

negative regulation of MAP kinase activity

17244894

HgeneBMP4

GO:0045606

positive regulation of epidermal cell differentiation

18823971

HgeneBMP4

GO:0045662

negative regulation of myoblast differentiation

14749725

HgeneBMP4

GO:0045669

positive regulation of osteoblast differentiation

14749725|18436533

HgeneBMP4

GO:0045778

positive regulation of ossification

14749725

HgeneBMP4

GO:0045786

negative regulation of cell cycle

11502704

HgeneBMP4

GO:0045839

negative regulation of mitotic nuclear division

17244894

HgeneBMP4

GO:0045843

negative regulation of striated muscle tissue development

14749725

HgeneBMP4

GO:0045892

negative regulation of transcription, DNA-templated

10706139|12631064|17244894

HgeneBMP4

GO:0045893

positive regulation of transcription, DNA-templated

10021330|17600318|17992660

HgeneBMP4

GO:0045944

positive regulation of transcription by RNA polymerase II

9187146|15516325

HgeneBMP4

GO:0048286

lung alveolus development

8674409

HgeneBMP4

GO:0048392

intermediate mesodermal cell differentiation

10021330

HgeneBMP4

GO:0048661

positive regulation of smooth muscle cell proliferation

10706139|17600318

HgeneBMP4

GO:0048754

branching morphogenesis of an epithelial tube

10706139

HgeneBMP4

GO:0050679

positive regulation of epithelial cell proliferation

11865031

HgeneBMP4

GO:0060391

positive regulation of SMAD protein signal transduction

9389648

HgeneBMP4

GO:0060393

regulation of pathway-restricted SMAD protein phosphorylation

18787191

HgeneBMP4

GO:0060395

SMAD protein signal transduction

17244894

HgeneBMP4

GO:0060425

lung morphogenesis

8674409

HgeneBMP4

GO:0060433

bronchus development

8674409

HgeneBMP4

GO:0060438

trachea development

8674409

HgeneBMP4

GO:0060441

epithelial tube branching involved in lung morphogenesis

8674409

HgeneBMP4

GO:0060502

epithelial cell proliferation involved in lung morphogenesis

8674409

HgeneBMP4

GO:0060503

bud dilation involved in lung branching

8674409

HgeneBMP4

GO:0060548

negative regulation of cell death

12631064

HgeneBMP4

GO:0061036

positive regulation of cartilage development

3201241

HgeneBMP4

GO:0061155

pulmonary artery endothelial tube morphogenesis

17992660

HgeneBMP4

GO:0071893

BMP signaling pathway involved in nephric duct formation

10021330

HgeneBMP4

GO:0072097

negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway

10706139|17118062

HgeneBMP4

GO:0072101

specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway

10706139|17118062

HgeneBMP4

GO:0072125

negative regulation of glomerular mesangial cell proliferation

17244894

HgeneBMP4

GO:0072200

negative regulation of mesenchymal cell proliferation involved in ureter development

12399320

HgeneBMP4

GO:0090184

positive regulation of kidney development

10021330

HgeneBMP4

GO:0090191

negative regulation of branching involved in ureteric bud morphogenesis

12141440|17118062

HgeneBMP4

GO:0090194

negative regulation of glomerulus development

12141440

HgeneBMP4

GO:1902894

negative regulation of pri-miRNA transcription by RNA polymerase II

28124060

HgeneBMP4

GO:1903800

positive regulation of production of miRNAs involved in gene silencing by miRNA

18548003

HgeneBMP4

GO:2000005

negative regulation of metanephric S-shaped body morphogenesis

12141440

HgeneBMP4

GO:2000007

negative regulation of metanephric comma-shaped body morphogenesis

12141440


check buttonFusion gene breakpoints across BMP4 (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 LRR1 (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-HU-8244-01ABMP4chr14

54423268

-LRR1chr14

50069088

+


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Fusion Gene ORF analysis for BMP4-LRR1

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-3CDSENST00000245451ENST00000298288BMP4chr14

54423268

-LRR1chr14

50069088

+
5UTR-3CDSENST00000245451ENST00000318317BMP4chr14

54423268

-LRR1chr14

50069088

+
5UTR-3CDSENST00000558489ENST00000298288BMP4chr14

54423268

-LRR1chr14

50069088

+
5UTR-3CDSENST00000558489ENST00000318317BMP4chr14

54423268

-LRR1chr14

50069088

+
5UTR-intronENST00000245451ENST00000557531BMP4chr14

54423268

-LRR1chr14

50069088

+
5UTR-intronENST00000558489ENST00000557531BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-3CDSENST00000417573ENST00000298288BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-3CDSENST00000417573ENST00000318317BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-3CDSENST00000558984ENST00000298288BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-3CDSENST00000558984ENST00000318317BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-3CDSENST00000559087ENST00000298288BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-3CDSENST00000559087ENST00000318317BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-intronENST00000417573ENST00000557531BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-intronENST00000558984ENST00000557531BMP4chr14

54423268

-LRR1chr14

50069088

+
intron-intronENST00000559087ENST00000557531BMP4chr14

54423268

-LRR1chr14

50069088

+

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 BMP4-LRR1


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)
BMP4chr1454423267-LRR1chr1450069087+0.0174977650.9825022
BMP4chr1454423267-LRR1chr1450069087+0.0174977650.9825022

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.
genomic feature of top 1%

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Fusion Protein Features for BMP4-LRR1


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/:54423268/:50069088)
- 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
BMP4

P12644

LRR1

Q96L50

FUNCTION: Induces cartilage and bone formation. Also acts in mesoderm induction, tooth development, limb formation and fracture repair. Acts in concert with PTHLH/PTHRP to stimulate ductal outgrowth during embryonic mammary development and to inhibit hair follicle induction (By similarity). {ECO:0000250}.FUNCTION: May negatively regulate the 4-1BB-mediated signaling cascades which result in the activation of NK-kappaB and JNK1. Probable substrate recognition subunit of an ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000269|PubMed:15601820}.

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 BMP4-LRR1


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 BMP4-LRR1


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 BMP4-LRR1


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 BMP4-LRR1


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