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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:PAFAH1B1-NTN1 (FusionGDB2 ID:61929)

Fusion Gene Summary for PAFAH1B1-NTN1

check button Fusion gene summary
Fusion gene informationFusion gene name: PAFAH1B1-NTN1
Fusion gene ID: 61929
HgeneTgene
Gene symbol

PAFAH1B1

NTN1

Gene ID

5048

9423

Gene nameplatelet activating factor acetylhydrolase 1b regulatory subunit 1netrin 1
SynonymsLIS1|LIS2|MDCR|MDS|NudF|PAFAHMRMV4|NTN1L
Cytomap

17p13.3

17p13.1

Type of geneprotein-codingprotein-coding
Descriptionplatelet-activating factor acetylhydrolase IB subunit alphalissencephaly 1 proteinplatelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)platelet-activatinnetrin-1epididymis tissue protein Li 131Pnetrin 1, mouse, homolog of
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000397195, ENST00000572915, 
ENST00000451360, 		ENST00000173229, 
ENST00000538852, ENST00000546090, 
Fusion gene scores* DoF score13 X 10 X 4=5205 X 7 X 3=105
# samples 147
** MAII scorelog2(14/520*10)=-1.89308479608349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/105*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PAFAH1B1 [Title/Abstract] AND NTN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPAFAH1B1(2497300)-NTN1(9066130), # 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
HgenePAFAH1B1

GO:0007017

microtubule-based process

11940666


check buttonFusion gene breakpoints across PAFAH1B1 (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 NTN1 (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
ChimerDB4OVTCGA-59-2352-01APAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
ChimerDB4OVTCGA-59-2352PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
ChimerDB4OVTCGA-59-2352-01APAFAH1B1chr17

2497300

+NTN1chr17

9066130

+


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Fusion Gene ORF analysis for PAFAH1B1-NTN1

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
5UTR-3CDSENST00000397195ENST00000173229PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
5UTR-3CDSENST00000397195ENST00000538852PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
5UTR-3CDSENST00000397195ENST00000546090PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
3UTR-3CDSENST00000572915ENST00000173229PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
3UTR-3CDSENST00000572915ENST00000538852PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
3UTR-3CDSENST00000572915ENST00000546090PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
intron-3CDSENST00000451360ENST00000173229PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
intron-3CDSENST00000451360ENST00000538852PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
intron-3CDSENST00000451360ENST00000546090PAFAH1B1chr17

2497300

+NTN1chr17

9066130

+
5UTR-3CDSENST00000397195ENST00000173229PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
5UTR-3CDSENST00000397195ENST00000538852PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
5UTR-3CDSENST00000397195ENST00000546090PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
3UTR-3CDSENST00000572915ENST00000173229PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
3UTR-3CDSENST00000572915ENST00000538852PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
3UTR-3CDSENST00000572915ENST00000546090PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
intron-3CDSENST00000451360ENST00000173229PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
intron-3CDSENST00000451360ENST00000538852PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+
intron-3CDSENST00000451360ENST00000546090PAFAH1B1chr17

2497300

+NTN1chr17

9066129

+

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 PAFAH1B1-NTN1


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)
PAFAH1B1chr172497300+NTN1chr179066129+1.08E-091
PAFAH1B1chr172497300+NTN1chr179066129+1.08E-091
PAFAH1B1chr172497300+NTN1chr179066129+1.08E-091
PAFAH1B1chr172497300+NTN1chr179066129+1.08E-091

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 PAFAH1B1-NTN1


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
..
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: 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.

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 PAFAH1B1-NTN1


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 PAFAH1B1-NTN1


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 PAFAH1B1-NTN1


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 PAFAH1B1-NTN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePAFAH1B1C0431375Classical Lissencephaly9GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgenePAFAH1B1C0036341Schizophrenia1PSYGENET
HgenePAFAH1B1C0265219Miller Dieker syndrome1ORPHANET
HgenePAFAH1B1C0596263Carcinogenesis1CTD_human
HgenePAFAH1B1C1848201Subcortical Band Heterotopia1GENOMICS_ENGLAND;ORPHANET
HgenePAFAH1B1C2750748Chromosome 17p13.3 Duplication Syndrome1ORPHANET
TgeneNTN1C0006114Cerebral Edema1CTD_human
TgeneNTN1C0038525Subarachnoid Hemorrhage1CTD_human
TgeneNTN1C0270192Perinatal Subarachnoid Hemorrhage1CTD_human
TgeneNTN1C0472383Subarachnoid Hemorrhage, Spontaneous1CTD_human
TgeneNTN1C0472387Vasogenic Cerebral Edema1CTD_human
TgeneNTN1C0472388Cytotoxic Cerebral Edema1CTD_human
TgeneNTN1C0525041Neurobehavioral Manifestations1CTD_human
TgeneNTN1C0750969Vasogenic Brain Edema1CTD_human
TgeneNTN1C0750970Cytotoxic Brain Edema1CTD_human
TgeneNTN1C0751530Subarachnoid Hemorrhage, Aneurysmal1CTD_human
TgeneNTN1C0795688Subarachnoid Hemorrhage, Intracranial1CTD_human
TgeneNTN1C1527311Brain Edema1CTD_human
TgeneNTN1C4748869MIRROR MOVEMENTS 41UNIPROT