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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:APOLD1-CDKN1B (FusionGDB2 ID:HG81575TG1027)

Fusion Gene Summary for APOLD1-CDKN1B

check button Fusion gene summary
Fusion gene informationFusion gene name: APOLD1-CDKN1B
Fusion gene ID: hg81575tg1027
HgeneTgene
Gene symbol

APOLD1

CDKN1B

Gene ID

81575

1027

Gene nameapolipoprotein L domain containing 1cyclin dependent kinase inhibitor 1B
SynonymsVERGECDKN4|KIP1|MEN1B|MEN4|P27KIP1
Cytomap('APOLD1')('CDKN1B')

12p13.1

12p13.1

Type of geneprotein-codingprotein-coding
Descriptionapolipoprotein L domain-containing protein 1vascular early response gene proteincyclin-dependent kinase inhibitor 1Bcyclin-dependent kinase inhibitor 1B (p27, Kip1)
Modification date2020031320200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000326765, ENST00000356591, 
Fusion gene scores* DoF score5 X 4 X 4=805 X 5 X 2=50
# samples 55
** MAII scorelog2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/50*10)=0
Context

PubMed: APOLD1 [Title/Abstract] AND CDKN1B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPOLD1(12879030)-CDKN1B(12873970), # samples:3
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
TgeneCDKN1B

GO:0000082

G1/S transition of mitotic cell cycle

10208428

TgeneCDKN1B

GO:0008285

negative regulation of cell proliferation

19266349

TgeneCDKN1B

GO:0010942

positive regulation of cell death

19266349

TgeneCDKN1B

GO:0030308

negative regulation of cell growth

10208428

TgeneCDKN1B

GO:0033673

negative regulation of kinase activity

19170105

TgeneCDKN1B

GO:0042326

negative regulation of phosphorylation

10208428

TgeneCDKN1B

GO:0045732

positive regulation of protein catabolic process

19056892

TgeneCDKN1B

GO:0045736

negative regulation of cyclin-dependent protein serine/threonine kinase activity

28666995

TgeneCDKN1B

GO:0045892

negative regulation of transcription, DNA-templated

19170105

TgeneCDKN1B

GO:0045930

negative regulation of mitotic cell cycle

19266349

TgeneCDKN1B

GO:0048102

autophagic cell death

12698196

TgeneCDKN1B

GO:0071285

cellular response to lithium ion

19056892

TgeneCDKN1B

GO:0071850

mitotic cell cycle arrest

19266349



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
ChimerDB4BRCATCGA-AQ-A04J-01AAPOLD1chr12

12879030

-CDKN1Bchr12

12873970

+
ChimerDB4BRCATCGA-AQ-A04J-01AAPOLD1chr12

12879030

+CDKN1Bchr12

12873970

+


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Fusion Gene ORF analysis for APOLD1-CDKN1B

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-3UTRENST00000326765ENST00000228872APOLD1chr12

12879030

+CDKN1Bchr12

12873970

+
5CDS-3UTRENST00000326765ENST00000477087APOLD1chr12

12879030

+CDKN1Bchr12

12873970

+
5CDS-intronENST00000326765ENST00000396340APOLD1chr12

12879030

+CDKN1Bchr12

12873970

+
intron-3UTRENST00000356591ENST00000228872APOLD1chr12

12879030

+CDKN1Bchr12

12873970

+
intron-3UTRENST00000356591ENST00000477087APOLD1chr12

12879030

+CDKN1Bchr12

12873970

+
intron-intronENST00000356591ENST00000396340APOLD1chr12

12879030

+CDKN1Bchr12

12873970

+

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 APOLD1-CDKN1B


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)
APOLD1chr1212879030+CDKN1Bchr1212873969+0.95363020.046369813
APOLD1chr1212879030+CDKN1Bchr1212873969+0.95363020.046369813


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 APOLD1-CDKN1B


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/:12879030/:12873970)
- 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 APOLD1-CDKN1B


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 APOLD1-CDKN1B


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 APOLD1-CDKN1B


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 APOLD1-CDKN1B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1970712Multiple Endocrine Neoplasia, Type IV11CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC4274947Multiple endocrine neoplasia type 49CLINGEN
TgeneC0009405Hereditary Nonpolyposis Colorectal Neoplasms8CLINGEN
TgeneC1112155Hereditary non-polyposis colorectal cancer syndrome8CLINGEN
TgeneC1333990Hereditary Nonpolyposis Colorectal Cancer8CLINGEN
TgeneC1333991Hereditary Non-Polyposis Colon Cancer Type 28CLINGEN
TgeneC2936783Colorectal cancer, hereditary nonpolyposis, type 18CLINGEN
TgeneC0024121Lung Neoplasms3CTD_human
TgeneC0033578Prostatic Neoplasms3CTD_human
TgeneC0242379Malignant neoplasm of lung3CTD_human
TgeneC0376358Malignant neoplasm of prostate3CTD_human
TgeneC0025267Multiple Endocrine Neoplasia Type 12ORPHANET
TgeneC0032000Pituitary Adenoma2CGI;CTD_human;GENOMICS_ENGLAND
TgeneC0006142Malignant neoplasm of breast1CGI;CTD_human
TgeneC0007113Rectal Carcinoma1CTD_human
TgeneC0021841Intestinal Neoplasms1CTD_human
TgeneC0022665Kidney Neoplasm1CTD_human
TgeneC0023903Liver neoplasms1CTD_human
TgeneC0024623Malignant neoplasm of stomach1CTD_human
TgeneC0025500Mesothelioma1CTD_human
TgeneC0032019Pituitary Neoplasms1CTD_human
TgeneC0034885Rectal Neoplasms1CTD_human
TgeneC0036920Sezary Syndrome1CTD_human
TgeneC0038356Stomach Neoplasms1CTD_human
TgeneC0042138Uterine Neoplasms1CTD_human
TgeneC0079487Helicobacter Infections1CTD_human
TgeneC0153567Uterine Cancer1CTD_human
TgeneC0206669Hepatocellular Adenoma1CTD_human
TgeneC0206754Neuroendocrine Tumors1CTD_human
TgeneC0263454Chloracne1CTD_human
TgeneC0282612Prostatic Intraepithelial Neoplasias1CTD_human
TgeneC0345904Malignant neoplasm of liver1CTD_human
TgeneC0346300Pituitary carcinoma1CTD_human
TgeneC0346627Intestinal Cancer1CTD_human
TgeneC0549473Thyroid carcinoma1GENOMICS_ENGLAND
TgeneC0678222Breast Carcinoma1CGI;CTD_human
TgeneC0740457Malignant neoplasm of kidney1CTD_human
TgeneC0919267ovarian neoplasm1CTD_human
TgeneC1140680Malignant neoplasm of ovary1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneC2239176Liver carcinoma1CTD_human
TgeneC2931456Prostate cancer, familial1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human
TgeneC4722327PROSTATE CANCER, HEREDITARY, 11CTD_human