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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:NDE1-C16orf45 (FusionGDB2 ID:57574)

Fusion Gene Summary for NDE1-C16orf45

check button Fusion gene summary
Fusion gene informationFusion gene name: NDE1-C16orf45
Fusion gene ID: 57574
HgeneTgene
Gene symbol

NDE1

C16orf45

Gene ID

54820

89927

Gene namenudE neurodevelopment protein 1bMERB domain containing 1
SynonymsHOM-TES-87|LIS4|MHAC|NDE|NUDE|NUDE1C16orf45|MINP
Cytomap

16p13.11

16p13.11

Type of geneprotein-codingprotein-coding
Descriptionnuclear distribution protein nudE homolog 1LIS1-interacting protein NUDE1, rat homologepididymis secretory sperm binding proteinnudE nuclear distribution E homolog 1nudE nuclear distribution gene E homolog 1bMERB domain-containing protein 1migration inhibitory proteinuncharacterized protein C16orf45
Modification date2020031320200313
UniProtAcc

Q9NXR1

.
Ensembl transtripts involved in fusion geneENST00000396353, ENST00000396355, 
ENST00000396354, ENST00000342673, 
ENST00000571896, 		ENST00000300006, 
ENST00000566490, ENST00000452191, 
ENST00000561692, ENST00000565913, 
Fusion gene scores* DoF score13 X 15 X 5=97514 X 11 X 8=1232
# samples 1616
** MAII scorelog2(16/975*10)=-2.60733031374961
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1232*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NDE1 [Title/Abstract] AND C16orf45 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNDE1(15790717)-C16orf45(15609161), # samples:1
Anticipated loss of major functional domain due to fusion event.NDE1-C16orf45 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
* 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

check buttonFusion gene breakpoints across NDE1 (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 C16orf45 (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
ChimerDB4ESCATCGA-2H-A9GNNDE1chr16

15790717

+C16orf45chr16

15609161

+


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Fusion Gene ORF analysis for NDE1-C16orf45

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
Frame-shiftENST00000396353ENST00000300006NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000396353ENST00000566490NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000396353ENST00000452191NDE1chr16

15790717

+C16orf45chr16

15609161

+
5CDS-intronENST00000396353ENST00000561692NDE1chr16

15790717

+C16orf45chr16

15609161

+
5CDS-intronENST00000396353ENST00000565913NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000396355ENST00000300006NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000396355ENST00000566490NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000396355ENST00000452191NDE1chr16

15790717

+C16orf45chr16

15609161

+
5CDS-intronENST00000396355ENST00000561692NDE1chr16

15790717

+C16orf45chr16

15609161

+
5CDS-intronENST00000396355ENST00000565913NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000396354ENST00000300006NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000396354ENST00000566490NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000396354ENST00000452191NDE1chr16

15790717

+C16orf45chr16

15609161

+
5CDS-intronENST00000396354ENST00000561692NDE1chr16

15790717

+C16orf45chr16

15609161

+
5CDS-intronENST00000396354ENST00000565913NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000342673ENST00000300006NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000342673ENST00000566490NDE1chr16

15790717

+C16orf45chr16

15609161

+
Frame-shiftENST00000342673ENST00000452191NDE1chr16

15790717

+C16orf45chr16

15609161

+
5CDS-intronENST00000342673ENST00000561692NDE1chr16

15790717

+C16orf45chr16

15609161

+
5CDS-intronENST00000342673ENST00000565913NDE1chr16

15790717

+C16orf45chr16

15609161

+
intron-3CDSENST00000571896ENST00000300006NDE1chr16

15790717

+C16orf45chr16

15609161

+
intron-3CDSENST00000571896ENST00000566490NDE1chr16

15790717

+C16orf45chr16

15609161

+
intron-3CDSENST00000571896ENST00000452191NDE1chr16

15790717

+C16orf45chr16

15609161

+
intron-intronENST00000571896ENST00000561692NDE1chr16

15790717

+C16orf45chr16

15609161

+
intron-intronENST00000571896ENST00000565913NDE1chr16

15790717

+C16orf45chr16

15609161

+

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 NDE1-C16orf45


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)
NDE1chr1615790717+C16orf45chr1615609161+5.65E-060.9999944
NDE1chr1615790717+C16orf45chr1615609161+5.65E-060.9999944

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 NDE1-C16orf45


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
NDE1

Q9NXR1

.
FUNCTION: Required for centrosome duplication and formation and function of the mitotic spindle. Essential for the development of the cerebral cortex. May regulate the production of neurons by controlling the orientation of the mitotic spindle during division of cortical neuronal progenitors of the proliferative ventricular zone of the brain. Orientation of the division plane perpendicular to the layers of the cortex gives rise to two proliferative neuronal progenitors whereas parallel orientation of the division plane yields one proliferative neuronal progenitor and a post-mitotic neuron. A premature shift towards a neuronal fate within the progenitor population may result in an overall reduction in the final number of neurons and an increase in the number of neurons in the deeper layers of the cortex. {ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:21529752}.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 NDE1-C16orf45


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 NDE1-C16orf45


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 NDE1-C16orf45


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 NDE1-C16orf45


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNDE1C0036341Schizophrenia4PSYGENET
HgeneNDE1C1857977MICROHYDRANENCEPHALY2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneNDE1C1956147Microlissencephaly2ORPHANET
HgeneNDE1C3151461LISSENCEPHALY 42GENOMICS_ENGLAND
HgeneNDE1C0020225Hydranencephaly1ORPHANET
HgeneNDE1C0033975Psychotic Disorders1PSYGENET
HgeneNDE1C0349204Nonorganic psychosis1PSYGENET
HgeneNDE1C0431350Primary microcephaly1GENOMICS_ENGLAND