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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:BPIFC-ALDH1A1 (FusionGDB2 ID:10075)

Fusion Gene Summary for BPIFC-ALDH1A1

check button Fusion gene summary
Fusion gene informationFusion gene name: BPIFC-ALDH1A1
Fusion gene ID: 10075
HgeneTgene
Gene symbol

BPIFC

ALDH1A1

Gene ID

254240

216

Gene nameBPI fold containing family Caldehyde dehydrogenase 1 family member A1
SynonymsBPIL2ALDC|ALDH-E1|ALDH1|ALDH11|HEL-9|HEL-S-53e|HEL12|PUMB1|RALDH1
Cytomap

22q12.3

9q21.13

Type of geneprotein-codingprotein-coding
DescriptionBPI fold-containing family C proteinBPI-like 2bactericidal/permeability-increasing protein-like 2retinal dehydrogenase 1ALDH class 1ALHDIIRALDH 1acetaldehyde dehydrogenase 1aldehyde dehydrogenase 1, solublealdehyde dehydrogenase, liver cytosolicepididymis luminal protein 12epididymis luminal protein 9epididymis secretory sperm binding protei
Modification date2020031320200313
UniProtAcc

Q8NFQ6

P00352

Ensembl transtripts involved in fusion geneENST00000300399, ENST00000397450, 
ENST00000397452, ENST00000432451, 
ENST00000534972, 		ENST00000297785, 
ENST00000376939, ENST00000482210, 
Fusion gene scores* DoF score1 X 1 X 1=18 X 11 X 3=264
# samples 112
** MAII scorelog2(1/1*10)=3.32192809488736log2(12/264*10)=-1.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BPIFC [Title/Abstract] AND ALDH1A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBPIFC(32825527)-ALDH1A1(75515587), # 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
TgeneALDH1A1

GO:0055114

oxidation-reduction process

25450233


check buttonFusion gene breakpoints across BPIFC (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 ALDH1A1 (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/ACB048852BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+


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Fusion Gene ORF analysis for BPIFC-ALDH1A1

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-3UTRENST00000300399ENST00000297785BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-3UTRENST00000397450ENST00000297785BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-3UTRENST00000397452ENST00000297785BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-3UTRENST00000432451ENST00000297785BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-3UTRENST00000534972ENST00000297785BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000300399ENST00000376939BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000300399ENST00000482210BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000397450ENST00000376939BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000397450ENST00000482210BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000397452ENST00000376939BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000397452ENST00000482210BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000432451ENST00000376939BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000432451ENST00000482210BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000534972ENST00000376939BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+
intron-intronENST00000534972ENST00000482210BPIFCchr22

32825527

+ALDH1A1chr9

75515587

+

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 BPIFC-ALDH1A1


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 BPIFC-ALDH1A1


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/:32825527/:75515587)
- 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
BPIFC

Q8NFQ6

ALDH1A1

P00352

FUNCTION: Can convert/oxidize retinaldehyde to retinoic acid. Binds free retinal and cellular retinol-binding protein-bound retinal (By similarity). May have a broader specificity and oxidize other aldehydes in vivo (PubMed:19296407, PubMed:26373694, PubMed:25450233). {ECO:0000250|UniProtKB:P51647, ECO:0000269|PubMed:19296407, ECO:0000269|PubMed:25450233, ECO:0000269|PubMed:26373694}.

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 BPIFC-ALDH1A1


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 BPIFC-ALDH1A1


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 BPIFC-ALDH1A1


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 BPIFC-ALDH1A1


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