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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:ATF3-CDH20 (FusionGDB2 ID:HG467TG28316)

Fusion Gene Summary for ATF3-CDH20

check button Fusion gene summary
Fusion gene informationFusion gene name: ATF3-CDH20
Fusion gene ID: hg467tg28316
HgeneTgene
Gene symbol

ATF3

CDH20

Gene ID

467

28316

Gene nameactivating transcription factor 3cadherin 20
Synonyms-CDH7L3|Cdh7
Cytomap('ATF3')('CDH20')

1q32.3

18q21.33

Type of geneprotein-codingprotein-coding
Descriptioncyclic AMP-dependent transcription factor ATF-3cAMP-dependent transcription factor ATF-3cadherin-20cadherin 20, type 2
Modification date2020032220200313
UniProtAcc

P18847

.
Ensembl transtripts involved in fusion geneENST00000336937, ENST00000341491, 
ENST00000366983, ENST00000366985, 
ENST00000366987, ENST00000492118, 
Fusion gene scores* DoF score3 X 2 X 3=182 X 2 X 2=8
# samples 32
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(2/8*10)=1.32192809488736
Context

PubMed: ATF3 [Title/Abstract] AND CDH20 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATF3(212791576)-CDH20(59157635), # 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
HgeneATF3

GO:0000122

negative regulation of transcription by RNA polymerase II

8622660

HgeneATF3

GO:0045944

positive regulation of transcription by RNA polymerase II

16300731

HgeneATF3

GO:1990440

positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress

24939851



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
ChimerDB4LUSCTCGA-22-5483-01AATF3chr1

212791576

-CDH20chr18

59157635

+
ChimerDB4LUSCTCGA-22-5483-01AATF3chr1

212791576

+CDH20chr18

59157635

+


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Fusion Gene ORF analysis for ATF3-CDH20

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-5UTRENST00000336937ENST00000262717ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000336937ENST00000538374ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000341491ENST00000262717ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000341491ENST00000538374ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000366983ENST00000262717ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000366983ENST00000538374ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000366985ENST00000262717ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000366985ENST00000538374ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000366987ENST00000262717ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-5UTRENST00000366987ENST00000538374ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-intronENST00000336937ENST00000536675ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-intronENST00000341491ENST00000536675ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-intronENST00000366983ENST00000536675ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-intronENST00000366985ENST00000536675ATF3chr1

212791576

+CDH20chr18

59157635

+
5CDS-intronENST00000366987ENST00000536675ATF3chr1

212791576

+CDH20chr18

59157635

+
intron-5UTRENST00000492118ENST00000262717ATF3chr1

212791576

+CDH20chr18

59157635

+
intron-5UTRENST00000492118ENST00000538374ATF3chr1

212791576

+CDH20chr18

59157635

+
intron-intronENST00000492118ENST00000536675ATF3chr1

212791576

+CDH20chr18

59157635

+

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 ATF3-CDH20


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)
ATF3chr1212791576+CDH20chr1859157634+0.0001295080.9998704
ATF3chr1212791576+CDH20chr1859157634+0.0001295080.9998704


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 ATF3-CDH20


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/:212791576/:59157635)
- 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
ATF3

P18847

.
FUNCTION: This protein binds the cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'), a sequence present in many viral and cellular promoters. Represses transcription from promoters with ATF sites. It may repress transcription by stabilizing the binding of inhibitory cofactors at the promoter. {ECO:0000269|PubMed:7515060}.; FUNCTION: [Isoform 2]: Activates transcription presumably by sequestering inhibitory cofactors away from the promoters. {ECO:0000269|PubMed:7515060}.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 ATF3-CDH20


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 ATF3-CDH20


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 ATF3-CDH20


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 ATF3-CDH20


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATF3C0027765nervous system disorder2CTD_human
HgeneATF3C0002152Alloxan Diabetes1CTD_human
HgeneATF3C0007131Non-Small Cell Lung Carcinoma1CTD_human
HgeneATF3C0011570Mental Depression1PSYGENET
HgeneATF3C0011581Depressive disorder1PSYGENET
HgeneATF3C0011853Diabetes Mellitus, Experimental1CTD_human
HgeneATF3C0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
HgeneATF3C0021400Influenza1CTD_human
HgeneATF3C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneATF3C0023903Liver neoplasms1CTD_human
HgeneATF3C0033141Cardiomyopathies, Primary1CTD_human
HgeneATF3C0033578Prostatic Neoplasms1CTD_human
HgeneATF3C0036529Myocardial Diseases, Secondary1CTD_human
HgeneATF3C0038433Streptozotocin Diabetes1CTD_human
HgeneATF3C0238281Middle Cerebral Artery Syndrome1CTD_human
HgeneATF3C0345904Malignant neoplasm of liver1CTD_human
HgeneATF3C0376358Malignant neoplasm of prostate1CTD_human
HgeneATF3C0740376Middle Cerebral Artery Thrombosis1CTD_human
HgeneATF3C0740391Middle Cerebral Artery Occlusion1CTD_human
HgeneATF3C0740392Infarction, Middle Cerebral Artery1CTD_human
HgeneATF3C0751845Middle Cerebral Artery Embolus1CTD_human
HgeneATF3C0751846Left Middle Cerebral Artery Infarction1CTD_human
HgeneATF3C0751847Embolic Infarction, Middle Cerebral Artery1CTD_human
HgeneATF3C0751848Thrombotic Infarction, Middle Cerebral Artery1CTD_human
HgeneATF3C0751849Right Middle Cerebral Artery Infarction1CTD_human
HgeneATF3C0848558Hypospadias1CTD_human
HgeneATF3C0878544Cardiomyopathies1CTD_human
HgeneATF3C0919267ovarian neoplasm1CTD_human
HgeneATF3C1140680Malignant neoplasm of ovary1CTD_human
HgeneATF3C4721453Peripheral Nervous System Diseases1CTD_human