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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:PGA4-LIPF (FusionGDB2 ID:64106)

Fusion Gene Summary for PGA4-LIPF

check button Fusion gene summary
Fusion gene informationFusion gene name: PGA4-LIPF
Fusion gene ID: 64106
HgeneTgene
Gene symbol

PGA4

LIPF

Gene ID

643847

8513

Gene namepepsinogen A4lipase F, gastric type
Synonyms-GL|HGL|HLAL
Cytomap

11q12.2

10q23.31

Type of geneprotein-codingprotein-coding
Descriptionpepsin A-4pepsinogen 4, group I (pepsinogen A)pepsinogen-4pregnancy-associated glycoproteingastric triacylglycerol lipasegastric lipaselipase, gastric
Modification date2020031320200313
UniProtAcc.

P07098

Ensembl transtripts involved in fusion geneENST00000378149, ENST00000422676, 
ENST00000537932, ENST00000544899, 
ENST00000394375, ENST00000608620, 
ENST00000238983, ENST00000355843, 
Fusion gene scores* DoF score7 X 10 X 3=21017 X 18 X 7=2142
# samples 918
** MAII scorelog2(9/210*10)=-1.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/2142*10)=-3.57288966842058
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PGA4 [Title/Abstract] AND LIPF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIPF(90429618)-PGA4(60989825), # samples:2
LIPF(90438248)-PGA4(60999099), # samples:2
LIPF(90429623)-PGA4(60970994), # samples:2
LIPF(90436038)-PGA4(61017222), # samples:2
PGA4(60997697)-LIPF(90438381), # samples:2
Anticipated loss of major functional domain due to fusion event.LIPF-PGA4 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
LIPF-PGA4 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PGA4-LIPF seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PGA4-LIPF seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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

check buttonFusion gene breakpoints across PGA4 (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 LIPF (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
ChimerDB4ESCATCGA-L5-A43CPGA4chr11

60997697

+LIPFchr10

90438381

+
ChimerDB4ESCATCGA-L5-A43CPGA4chr11

60993853

+LIPFchr10

90424220

+
ChimerDB4ESCATCGA-L5-A4OJPGA4chr11

60999169

+LIPFchr10

90438428

+
ChimerDB4ESCATCGA-L5-A4ORPGA4chr11

60997697

+LIPFchr10

90438381

+


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Fusion Gene ORF analysis for PGA4-LIPF

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
Frame-shiftENST00000378149ENST00000394375PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000378149ENST00000608620PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000378149ENST00000238983PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000378149ENST00000355843PGA4chr11

60997697

+LIPFchr10

90438381

+
intron-3CDSENST00000422676ENST00000394375PGA4chr11

60997697

+LIPFchr10

90438381

+
intron-3CDSENST00000422676ENST00000608620PGA4chr11

60997697

+LIPFchr10

90438381

+
intron-3CDSENST00000422676ENST00000238983PGA4chr11

60997697

+LIPFchr10

90438381

+
intron-3CDSENST00000422676ENST00000355843PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000537932ENST00000394375PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000537932ENST00000608620PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000537932ENST00000238983PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000537932ENST00000355843PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000544899ENST00000394375PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000544899ENST00000608620PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000544899ENST00000238983PGA4chr11

60997697

+LIPFchr10

90438381

+
Frame-shiftENST00000544899ENST00000355843PGA4chr11

60997697

+LIPFchr10

90438381

+
5CDS-5UTRENST00000378149ENST00000394375PGA4chr11

60993853

+LIPFchr10

90424220

+
5CDS-5UTRENST00000378149ENST00000608620PGA4chr11

60993853

+LIPFchr10

90424220

+
5CDS-5UTRENST00000378149ENST00000238983PGA4chr11

60993853

+LIPFchr10

90424220

+
5CDS-5UTRENST00000378149ENST00000355843PGA4chr11

60993853

+LIPFchr10

90424220

+
5CDS-5UTRENST00000422676ENST00000394375PGA4chr11

60993853

+LIPFchr10

90424220

+
5CDS-5UTRENST00000422676ENST00000608620PGA4chr11

60993853

+LIPFchr10

90424220

+
5CDS-5UTRENST00000422676ENST00000238983PGA4chr11

60993853

+LIPFchr10

90424220

+
5CDS-5UTRENST00000422676ENST00000355843PGA4chr11

60993853

+LIPFchr10

90424220

+
intron-5UTRENST00000537932ENST00000394375PGA4chr11

60993853

+LIPFchr10

90424220

+
intron-5UTRENST00000537932ENST00000608620PGA4chr11

60993853

+LIPFchr10

90424220

+
intron-5UTRENST00000537932ENST00000238983PGA4chr11

60993853

+LIPFchr10

90424220

+
intron-5UTRENST00000537932ENST00000355843PGA4chr11

60993853

+LIPFchr10

90424220

+
intron-5UTRENST00000544899ENST00000394375PGA4chr11

60993853

+LIPFchr10

90424220

+
intron-5UTRENST00000544899ENST00000608620PGA4chr11

60993853

+LIPFchr10

90424220

+
intron-5UTRENST00000544899ENST00000238983PGA4chr11

60993853

+LIPFchr10

90424220

+
intron-5UTRENST00000544899ENST00000355843PGA4chr11

60993853

+LIPFchr10

90424220

+
3UTR-3CDSENST00000378149ENST00000394375PGA4chr11

60999169

+LIPFchr10

90438428

+
3UTR-3CDSENST00000378149ENST00000608620PGA4chr11

60999169

+LIPFchr10

90438428

+
3UTR-3CDSENST00000378149ENST00000238983PGA4chr11

60999169

+LIPFchr10

90438428

+
3UTR-3CDSENST00000378149ENST00000355843PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000422676ENST00000394375PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000422676ENST00000608620PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000422676ENST00000238983PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000422676ENST00000355843PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000537932ENST00000394375PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000537932ENST00000608620PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000537932ENST00000238983PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000537932ENST00000355843PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000544899ENST00000394375PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000544899ENST00000608620PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000544899ENST00000238983PGA4chr11

60999169

+LIPFchr10

90438428

+
intron-3CDSENST00000544899ENST00000355843PGA4chr11

60999169

+LIPFchr10

90438428

+

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 PGA4-LIPF


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 PGA4-LIPF


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

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

P07098

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Catalyzes the hydrolysis of triacylglycerols to yield free fatty acids, diacylglycerol, monoacylglycerol, and glycerol (PubMed:2243091, PubMed:10358049). Shows a preferential hydrolysis at the sn-3 position of triacylglycerol (PubMed:2243091). {ECO:0000269|PubMed:10358049, ECO:0000269|PubMed:2243091}.

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 PGA4-LIPF


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 PGA4-LIPF


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 PGA4-LIPF


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneLIPFP07098DB01083OrlistatInhibitorSmall moleculeApproved|Investigational

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Related Diseases for PGA4-LIPF


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