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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:CYP39A1-FGGY (FusionGDB2 ID:HG51302TG55277)

Fusion Gene Summary for CYP39A1-FGGY

check button Fusion gene summary
Fusion gene informationFusion gene name: CYP39A1-FGGY
Fusion gene ID: hg51302tg55277
HgeneTgene
Gene symbol

CYP39A1

FGGY

Gene ID

51302

55277

Gene namecytochrome P450 family 39 subfamily A member 1FGGY carbohydrate kinase domain containing
Synonyms--
Cytomap('CYP39A1')('FGGY')

6p12.3

1p32.1

Type of geneprotein-codingprotein-coding
Description24-hydroxycholesterol 7-alpha-hydroxylasecytochrome P450, family 39, subfamily A, polypeptide 1cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1FGGY carbohydrate kinase domain-containing proteinD-ribulokinase
Modification date2020031320200313
UniProtAcc

Q9NYL5

Q96C11

Ensembl transtripts involved in fusion geneENST00000275016, ENST00000489657, 
Fusion gene scores* DoF score3 X 3 X 3=2719 X 17 X 11=3553
# samples 324
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(24/3553*10)=-3.8879313777227
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CYP39A1 [Title/Abstract] AND FGGY [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCYP39A1(46609900)-FGGY(60223603), # samples:2
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
HgeneCYP39A1

GO:0006699

bile acid biosynthetic process

10748047

TgeneFGGY

GO:0019321

pentose metabolic process

27909055

TgeneFGGY

GO:0046835

carbohydrate phosphorylation

27909055



check button Fusion gene information
* 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
ChimerDB4PRADTCGA-EJ-8468-01ACYP39A1chr6

46609900

-FGGYchr1

60223603

+


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Fusion Gene ORF analysis for CYP39A1-FGGY

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
5CDS-intronENST00000275016ENST00000303721CYP39A1chr6

46609900

-FGGYchr1

60223603

+
5CDS-intronENST00000275016ENST00000371210CYP39A1chr6

46609900

-FGGYchr1

60223603

+
5CDS-intronENST00000275016ENST00000371212CYP39A1chr6

46609900

-FGGYchr1

60223603

+
5CDS-intronENST00000275016ENST00000371218CYP39A1chr6

46609900

-FGGYchr1

60223603

+
5CDS-intronENST00000275016ENST00000474476CYP39A1chr6

46609900

-FGGYchr1

60223603

+
intron-intronENST00000489657ENST00000303721CYP39A1chr6

46609900

-FGGYchr1

60223603

+
intron-intronENST00000489657ENST00000371210CYP39A1chr6

46609900

-FGGYchr1

60223603

+
intron-intronENST00000489657ENST00000371212CYP39A1chr6

46609900

-FGGYchr1

60223603

+
intron-intronENST00000489657ENST00000371218CYP39A1chr6

46609900

-FGGYchr1

60223603

+
intron-intronENST00000489657ENST00000474476CYP39A1chr6

46609900

-FGGYchr1

60223603

+

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 CYP39A1-FGGY


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)
CYP39A1chr646609899-FGGYchr160223602+0.0016765350.9983235
CYP39A1chr646609899-FGGYchr160223602+0.0016765350.9983235


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 CYP39A1-FGGY


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/:46609900/:60223603)
- 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
CYP39A1

Q9NYL5

FGGY

Q96C11

FUNCTION: A cytochrome P450 monooxygenase involved in neural cholesterol clearance through bile acid synthesis (PubMed:25201972, PubMed:10748047). Catalyzes 7-alpha hydroxylation of (24S)-hydroxycholesterol, a neural oxysterol that is metabolized to bile acids in the liver (PubMed:25201972, PubMed:10748047). Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (CPR; NADPH-ferrihemoprotein reductase) (PubMed:25201972, PubMed:10748047). {ECO:0000269|PubMed:10748047, ECO:0000269|PubMed:25201972}.

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 CYP39A1-FGGY


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 CYP39A1-FGGY


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 CYP39A1-FGGY


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 CYP39A1-FGGY


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCYP39A1C2239176Liver carcinoma1CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0043094Weight Gain1CTD_human