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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:NFKB1-PHF3 (FusionGDB2 ID:58617)

Fusion Gene Summary for NFKB1-PHF3

check button Fusion gene summary
Fusion gene informationFusion gene name: NFKB1-PHF3
Fusion gene ID: 58617
HgeneTgene
Gene symbol

NFKB1

PHF3

Gene ID

4790

23469

Gene namenuclear factor kappa B subunit 1PHD finger protein 3
SynonymsCVID12|EBP-1|KBF1|NF-kB|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50-
Cytomap

4q24

6q12

Type of geneprotein-codingprotein-coding
Descriptionnuclear factor NF-kappa-B p105 subunitDNA-binding factor KBF1NF-kappabetanuclear factor NF-kappa-B p50 subunitnuclear factor kappa-B DNA binding subunitnuclear factor of kappa light polypeptide gene enhancer in B-cells 1PHD finger protein 3
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000226574, ENST00000394820, 
ENST00000505458, ENST00000510638, 
ENST00000600343, 		ENST00000262043, 
ENST00000509330, ENST00000393387, 
ENST00000420043, 
Fusion gene scores* DoF score12 X 10 X 8=9605 X 6 X 4=120
# samples 126
** MAII scorelog2(12/960*10)=-3
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NFKB1 [Title/Abstract] AND PHF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNFKB1(103459113)-PHF3(64389900), # samples:1
Anticipated loss of major functional domain due to fusion event.NFKB1-PHF3 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
NFKB1-PHF3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
NFKB1-PHF3 seems lost the major protein functional domain in Tgene 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
HgeneNFKB1

GO:0010629

negative regulation of gene expression

26687115

HgeneNFKB1

GO:0010956

negative regulation of calcidiol 1-monooxygenase activity

15243130

HgeneNFKB1

GO:0045893

positive regulation of transcription, DNA-templated

17426251

HgeneNFKB1

GO:0045944

positive regulation of transcription by RNA polymerase II

1406630

HgeneNFKB1

GO:1900127

positive regulation of hyaluronan biosynthetic process

17324121


check buttonFusion gene breakpoints across NFKB1 (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 PHF3 (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-24-2254NFKB1chr4

103459113

+PHF3chr6

64389900

+


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Fusion Gene ORF analysis for NFKB1-PHF3

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-shiftENST00000226574ENST00000262043NFKB1chr4

103459113

+PHF3chr6

64389900

+
Frame-shiftENST00000226574ENST00000509330NFKB1chr4

103459113

+PHF3chr6

64389900

+
Frame-shiftENST00000226574ENST00000393387NFKB1chr4

103459113

+PHF3chr6

64389900

+
5CDS-intronENST00000226574ENST00000420043NFKB1chr4

103459113

+PHF3chr6

64389900

+
Frame-shiftENST00000394820ENST00000262043NFKB1chr4

103459113

+PHF3chr6

64389900

+
Frame-shiftENST00000394820ENST00000509330NFKB1chr4

103459113

+PHF3chr6

64389900

+
Frame-shiftENST00000394820ENST00000393387NFKB1chr4

103459113

+PHF3chr6

64389900

+
5CDS-intronENST00000394820ENST00000420043NFKB1chr4

103459113

+PHF3chr6

64389900

+
Frame-shiftENST00000505458ENST00000262043NFKB1chr4

103459113

+PHF3chr6

64389900

+
Frame-shiftENST00000505458ENST00000509330NFKB1chr4

103459113

+PHF3chr6

64389900

+
Frame-shiftENST00000505458ENST00000393387NFKB1chr4

103459113

+PHF3chr6

64389900

+
5CDS-intronENST00000505458ENST00000420043NFKB1chr4

103459113

+PHF3chr6

64389900

+
intron-3CDSENST00000510638ENST00000262043NFKB1chr4

103459113

+PHF3chr6

64389900

+
intron-3CDSENST00000510638ENST00000509330NFKB1chr4

103459113

+PHF3chr6

64389900

+
intron-3CDSENST00000510638ENST00000393387NFKB1chr4

103459113

+PHF3chr6

64389900

+
intron-intronENST00000510638ENST00000420043NFKB1chr4

103459113

+PHF3chr6

64389900

+
intron-3CDSENST00000600343ENST00000262043NFKB1chr4

103459113

+PHF3chr6

64389900

+
intron-3CDSENST00000600343ENST00000509330NFKB1chr4

103459113

+PHF3chr6

64389900

+
intron-3CDSENST00000600343ENST00000393387NFKB1chr4

103459113

+PHF3chr6

64389900

+
intron-intronENST00000600343ENST00000420043NFKB1chr4

103459113

+PHF3chr6

64389900

+

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 NFKB1-PHF3


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)
NFKB1chr4103459113+PHF3chr664389900+2.16E-101
NFKB1chr4103459113+PHF3chr664389900+2.16E-101

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 NFKB1-PHF3


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 NFKB1-PHF3


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 NFKB1-PHF3


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 NFKB1-PHF3


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 NFKB1-PHF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNFKB1C0001973Alcoholic Intoxication, Chronic4PSYGENET
HgeneNFKB1C0007102Malignant tumor of colon2CTD_human
HgeneNFKB1C0007621Neoplastic Cell Transformation2CTD_human
HgeneNFKB1C0009375Colonic Neoplasms2CTD_human
HgeneNFKB1C4225277IMMUNODEFICIENCY, COMMON VARIABLE, 122GENOMICS_ENGLAND
HgeneNFKB1C0001418Adenocarcinoma1CTD_human
HgeneNFKB1C0007786Brain Ischemia1CTD_human
HgeneNFKB1C0008312Primary biliary cirrhosis1CTD_human
HgeneNFKB1C0009447Common Variable Immunodeficiency1CTD_human;ORPHANET
HgeneNFKB1C0010093Corpus Luteum Cyst1CTD_human
HgeneNFKB1C0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
HgeneNFKB1C0020500Hyperoxaluria1CTD_human
HgeneNFKB1C0022660Kidney Failure, Acute1CTD_human
HgeneNFKB1C0022661Kidney Failure, Chronic1CTD_human
HgeneNFKB1C0023892Biliary cirrhosis1CTD_human
HgeneNFKB1C0023895Liver diseases1CTD_human
HgeneNFKB1C0029927Ovarian Cysts1CTD_human
HgeneNFKB1C0086565Liver Dysfunction1CTD_human
HgeneNFKB1C0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneNFKB1C0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneNFKB1C0205643Carcinoma, Cribriform1CTD_human
HgeneNFKB1C0205644Carcinoma, Granular Cell1CTD_human
HgeneNFKB1C0205645Adenocarcinoma, Tubular1CTD_human
HgeneNFKB1C0238065Secondary Biliary Cholangitis1CTD_human
HgeneNFKB1C0525045Mood Disorders1PSYGENET
HgeneNFKB1C0917798Cerebral Ischemia1CTD_human
HgeneNFKB1C1298681Oxalosis1CTD_human
HgeneNFKB1C1565662Acute Kidney Insufficiency1CTD_human
HgeneNFKB1C1846546Recurrent sinopulmonary infections1GENOMICS_ENGLAND
HgeneNFKB1C2609414Acute kidney injury1CTD_human
HgeneNFKB1C4551595Biliary Cirrhosis, Primary, 11CTD_human
TgenePHF3C0001973Alcoholic Intoxication, Chronic2PSYGENET