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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:SCG2-PTGS1 (FusionGDB2 ID:HG7857TG5742)

Fusion Gene Summary for SCG2-PTGS1

check button Fusion gene summary
Fusion gene informationFusion gene name: SCG2-PTGS1
Fusion gene ID: hg7857tg5742
HgeneTgene
Gene symbol

SCG2

PTGS1

Gene ID

7857

5742

Gene namesecretogranin IIprostaglandin-endoperoxide synthase 1
SynonymsCHGC|EM66|SN|SgIICOX1|COX3|PCOX1|PES-1|PGG/HS|PGHS-1|PGHS1|PHS1|PTGHS
Cytomap('SCG2')('PTGS1')

2q36.1

9q33.2

Type of geneprotein-codingprotein-coding
Descriptionsecretogranin-2chromogranin-Csecretoneurinprostaglandin G/H synthase 1PGH synthase 1cyclooxygenase-1prostaglandin H2 synthase 1prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000305409, 
Fusion gene scores* DoF score2 X 2 X 1=44 X 5 X 3=60
# samples 25
** MAII scorelog2(2/4*10)=2.32192809488736log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SCG2 [Title/Abstract] AND PTGS1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSCG2(224463684)-PTGS1(125140178), # 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
HgeneSCG2

GO:0000165

MAPK cascade

14970115

HgeneSCG2

GO:0001525

angiogenesis

14970115

HgeneSCG2

GO:0001938

positive regulation of endothelial cell proliferation

14970115

HgeneSCG2

GO:0035556

intracellular signal transduction

9473216

HgeneSCG2

GO:0048245

eosinophil chemotaxis

9473216

HgeneSCG2

GO:0050918

positive chemotaxis

9473216

HgeneSCG2

GO:0050930

induction of positive chemotaxis

9473216

HgeneSCG2

GO:2000352

negative regulation of endothelial cell apoptotic process

14970115

HgeneSCG2

GO:2001237

negative regulation of extrinsic apoptotic signaling pathway

14970115

TgenePTGS1

GO:0019371

cyclooxygenase pathway

1380156



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
ChimerDB4PCPGTCGA-QR-A6GR-01ASCG2chr2

224463684

-PTGS1chr9

125140178

+


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Fusion Gene ORF analysis for SCG2-PTGS1

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-3CDSENST00000305409ENST00000223423SCG2chr2

224463684

-PTGS1chr9

125140178

+
intron-3CDSENST00000305409ENST00000362012SCG2chr2

224463684

-PTGS1chr9

125140178

+
intron-3CDSENST00000305409ENST00000540753SCG2chr2

224463684

-PTGS1chr9

125140178

+
intron-5UTRENST00000305409ENST00000373698SCG2chr2

224463684

-PTGS1chr9

125140178

+

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 SCG2-PTGS1


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)


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Fusion Protein Features for SCG2-PTGS1


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/:224463684/:125140178)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 SCG2-PTGS1


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 SCG2-PTGS1


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 SCG2-PTGS1


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 SCG2-PTGS1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0021846Intestinal Polyps2CTD_human
TgeneC0038358Gastric ulcer2CTD_human
TgeneC0003873Rheumatoid Arthritis1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007097Carcinoma1CTD_human
TgeneC0010093Corpus Luteum Cyst1CTD_human
TgeneC0013182Drug Allergy1CTD_human
TgeneC0014859Esophageal Neoplasms1CTD_human
TgeneC0016382Flushing1CTD_human
TgeneC0018801Heart failure1CTD_human
TgeneC0018802Congestive heart failure1CTD_human
TgeneC0020429Hyperalgesia1CTD_human
TgeneC0022661Kidney Failure, Chronic1CTD_human
TgeneC0023212Left-Sided Heart Failure1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0029927Ovarian Cysts1CTD_human
TgeneC0035126Reperfusion Injury1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0037316Sleep Deprivation1CTD_human
TgeneC0085129Bronchial Hyperreactivity1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC0235527Heart Failure, Right-Sided1CTD_human
TgeneC0264423Asthma, Occupational1CTD_human
TgeneC0458247Allodynia1CTD_human
TgeneC0546837Malignant neoplasm of esophagus1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0751211Hyperalgesia, Primary1CTD_human
TgeneC0751212Hyperalgesia, Secondary1CTD_human
TgeneC0751213Tactile Allodynia1CTD_human
TgeneC0751214Hyperalgesia, Thermal1CTD_human
TgeneC0751505Insufficient Sleep Syndrome1CTD_human
TgeneC0751506REM Sleep Deprivation1CTD_human
TgeneC0751507Sleep Fragmentation1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1959583Myocardial Failure1CTD_human
TgeneC1961112Heart Decompensation1CTD_human
TgeneC2751535Prostaglandin-Endoperoxide Synthase 1 Deficiency, Platelet1GENOMICS_ENGLAND
TgeneC2936719Mechanical Allodynia1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human