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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:BMP7-LMF1 (FusionGDB2 ID:9882)

Fusion Gene Summary for BMP7-LMF1

check button Fusion gene summary
Fusion gene informationFusion gene name: BMP7-LMF1
Fusion gene ID: 9882
HgeneTgene
Gene symbol

BMP7

LMF1

Gene ID

655

64788

Gene namebone morphogenetic protein 7lipase maturation factor 1
SynonymsOP-1C16orf26|HMFN1876|JFP11|TMEM112|TMEM112A
Cytomap

20q13.31

16p13.3

Type of geneprotein-codingprotein-coding
Descriptionbone morphogenetic protein 7osteogenic protein 1lipase maturation factor 1transmembrane protein 112
Modification date2020032720200313
UniProtAcc

P18075

Q96S06

Ensembl transtripts involved in fusion geneENST00000395863, ENST00000395864, 
ENST00000450594, ENST00000460817, 
ENST00000262301, ENST00000399843, 
ENST00000543238, ENST00000539379, 
ENST00000568268, ENST00000568897, 
Fusion gene scores* DoF score11 X 10 X 6=6608 X 6 X 5=240
# samples 137
** MAII scorelog2(13/660*10)=-2.34395440121736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/240*10)=-1.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BMP7 [Title/Abstract] AND LMF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBMP7(55782899)-LMF1(904486), # 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
HgeneBMP7

GO:0010628

positive regulation of gene expression

28124060

HgeneBMP7

GO:0010800

positive regulation of peptidyl-threonine phosphorylation

19736306

HgeneBMP7

GO:0010862

positive regulation of pathway-restricted SMAD protein phosphorylation

9311995|16049014|17244894|19736306

HgeneBMP7

GO:0030501

positive regulation of bone mineralization

18436533

HgeneBMP7

GO:0030509

BMP signaling pathway

16049014|18436533

HgeneBMP7

GO:0034116

positive regulation of heterotypic cell-cell adhesion

15100360

HgeneBMP7

GO:0034504

protein localization to nucleus

17244894

HgeneBMP7

GO:0042326

negative regulation of phosphorylation

17244894

HgeneBMP7

GO:0043407

negative regulation of MAP kinase activity

17244894

HgeneBMP7

GO:0045665

negative regulation of neuron differentiation

16325379

HgeneBMP7

GO:0045669

positive regulation of osteoblast differentiation

18436533

HgeneBMP7

GO:0045786

negative regulation of cell cycle

11502704

HgeneBMP7

GO:0045839

negative regulation of mitotic nuclear division

17244894

HgeneBMP7

GO:0045892

negative regulation of transcription, DNA-templated

15100360|17244894

HgeneBMP7

GO:0045893

positive regulation of transcription, DNA-templated

14517293|15100360|16049014

HgeneBMP7

GO:0048762

mesenchymal cell differentiation

9693150

HgeneBMP7

GO:0048812

neuron projection morphogenesis

16325379

HgeneBMP7

GO:0060393

regulation of pathway-restricted SMAD protein phosphorylation

16049014

HgeneBMP7

GO:0060395

SMAD protein signal transduction

17244894

HgeneBMP7

GO:0060548

negative regulation of cell death

12631064

HgeneBMP7

GO:0070487

monocyte aggregation

15100360

HgeneBMP7

GO:0072125

negative regulation of glomerular mesangial cell proliferation

17244894

HgeneBMP7

GO:1900006

positive regulation of dendrite development

11580864

HgeneBMP7

GO:1900106

positive regulation of hyaluranon cable assembly

15100360


check buttonFusion gene breakpoints across BMP7 (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 LMF1 (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
ChiTaRS5.0N/ACB050414BMP7chr20

55782899

+LMF1chr16

904486

+


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Fusion Gene ORF analysis for BMP7-LMF1

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
intron-3UTRENST00000395863ENST00000262301BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000395863ENST00000399843BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000395863ENST00000543238BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000395864ENST00000262301BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000395864ENST00000399843BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000395864ENST00000543238BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000450594ENST00000262301BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000450594ENST00000399843BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000450594ENST00000543238BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000460817ENST00000262301BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000460817ENST00000399843BMP7chr20

55782899

+LMF1chr16

904486

+
intron-3UTRENST00000460817ENST00000543238BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000395863ENST00000539379BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000395863ENST00000568268BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000395863ENST00000568897BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000395864ENST00000539379BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000395864ENST00000568268BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000395864ENST00000568897BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000450594ENST00000539379BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000450594ENST00000568268BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000450594ENST00000568897BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000460817ENST00000539379BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000460817ENST00000568268BMP7chr20

55782899

+LMF1chr16

904486

+
intron-intronENST00000460817ENST00000568897BMP7chr20

55782899

+LMF1chr16

904486

+

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 BMP7-LMF1


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)

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.

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Fusion Protein Features for BMP7-LMF1


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/:55782899/:904486)
- 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
BMP7

P18075

LMF1

Q96S06

FUNCTION: Induces cartilage and bone formation. May be the osteoinductive factor responsible for the phenomenon of epithelial osteogenesis. Plays a role in calcium regulation and bone homeostasis. Promotes brown adipocyte differentiation by P38 MAPK pathway-mediated activation of target genes, including members of the SOX family of transcription factors (PubMed:27923061). {ECO:0000269|PubMed:27923061}.FUNCTION: Involved in the maturation of specific proteins in the endoplasmic reticulum. Required for maturation and transport of active lipoprotein lipase (LPL) through the secretory pathway. Each LMF1 molecule chaperones 50 or more molecules of LPL. {ECO:0000250|UniProtKB:Q3U3R4, ECO:0000269|PubMed:24909692}.

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 BMP7-LMF1


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 BMP7-LMF1


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 BMP7-LMF1


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 BMP7-LMF1


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