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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:PBX1-DHX40 (FusionGDB2 ID:62614)

Fusion Gene Summary for PBX1-DHX40

check button Fusion gene summary
Fusion gene informationFusion gene name: PBX1-DHX40
Fusion gene ID: 62614
HgeneTgene
Gene symbol

PBX1

DHX40

Gene ID

5087

79665

Gene namePBX homeobox 1DEAH-box helicase 40
SynonymsCAKUHEDARG147|DDX40|PAD
Cytomap

1q23.3

17q23.1

Type of geneprotein-codingprotein-coding
Descriptionpre-B-cell leukemia transcription factor 1homeobox protein PBX1homeobox protein PRLpre-B-cell leukemia homeobox 1probable ATP-dependent RNA helicase DHX40DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)DEAH (Asp-Glu-Ala-His) box polypeptide 40DEAH box protein 40
Modification date2020031320200313
UniProtAcc.

Q8IX18

Ensembl transtripts involved in fusion geneENST00000420696, ENST00000401534, 
ENST00000559240, ENST00000367897, 
ENST00000540236, ENST00000560641, 
ENST00000474046, ENST00000485769, 
ENST00000540246, 		ENST00000251241, 
ENST00000451169, ENST00000425628, 
Fusion gene scores* DoF score16 X 10 X 5=8007 X 6 X 2=84
# samples 218
** MAII scorelog2(21/800*10)=-1.9296106721086
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/84*10)=-0.070389327891398
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PBX1 [Title/Abstract] AND DHX40 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPBX1(164532548)-DHX40(57679883), # samples:3
Anticipated loss of major functional domain due to fusion event.PBX1-DHX40 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
PBX1-DHX40 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
PBX1-DHX40 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

check buttonFusion gene breakpoints across PBX1 (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 DHX40 (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
ChimerDB4BRCATCGA-E9-A22D-01APBX1chr1

164532548

+DHX40chr17

57679883

+
ChimerDB4BRCATCGA-E9-A22DPBX1chr1

164532548

+DHX40chr17

57679882

+
ChimerDB4BRCATCGA-E9-A22D-01APBX1chr1

164532548

+DHX40chr17

57679883

+
ChimerDB4BRCATCGA-E9-A22D-01APBX1chr1

164595333

+DHX40chr17

57679883

+
ChimerDB4BRCATCGA-E9-A22D-01APBX1chr1

164532548

-DHX40chr17

57679883

+


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Fusion Gene ORF analysis for PBX1-DHX40

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-shiftENST00000420696ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000420696ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000420696ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000401534ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000401534ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000401534ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000559240ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000559240ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000559240ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000367897ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000367897ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000367897ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000540236ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000540236ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000540236ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000560641ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000560641ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000560641ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000474046ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000474046ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000474046ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000485769ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000485769ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000485769ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000540246ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000540246ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679883

+
intron-3CDSENST00000540246ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679883

+
Frame-shiftENST00000420696ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000420696ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000420696ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000401534ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000401534ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000401534ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000559240ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000559240ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000559240ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000367897ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000367897ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000367897ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000540236ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000540236ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
Frame-shiftENST00000540236ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000560641ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000560641ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000560641ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000474046ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000474046ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000474046ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000485769ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000485769ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000485769ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000540246ENST00000251241PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000540246ENST00000451169PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000540246ENST00000425628PBX1chr1

164532548

+DHX40chr17

57679882

+
intron-3CDSENST00000420696ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000420696ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000420696ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000401534ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000401534ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000401534ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000559240ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000559240ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000559240ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000367897ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000367897ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000367897ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000540236ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000540236ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000540236ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+
5UTR-3CDSENST00000560641ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
5UTR-3CDSENST00000560641ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
5UTR-3CDSENST00000560641ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+
3UTR-3CDSENST00000474046ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
3UTR-3CDSENST00000474046ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
3UTR-3CDSENST00000474046ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000485769ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000485769ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000485769ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000540246ENST00000251241PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000540246ENST00000451169PBX1chr1

164595333

+DHX40chr17

57679883

+
intron-3CDSENST00000540246ENST00000425628PBX1chr1

164595333

+DHX40chr17

57679883

+

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 PBX1-DHX40


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)
PBX1chr1164595333+DHX40chr1757679882+0.0034114280.9965886
PBX1chr1164532548+DHX40chr1757679882+3.25E-050.99996746
PBX1chr1164532548+DHX40chr1757679882+3.25E-050.99996746
PBX1chr1164595333+DHX40chr1757679882+0.0034114280.9965886
PBX1chr1164532548+DHX40chr1757679882+3.25E-050.99996746
PBX1chr1164532548+DHX40chr1757679882+3.25E-050.99996746

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 PBX1-DHX40


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
.DHX40

Q8IX18

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: Probable ATP-dependent RNA helicase. {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 PBX1-DHX40


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 PBX1-DHX40


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 PBX1-DHX40


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 PBX1-DHX40


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePBX1C0006413Burkitt Lymphoma2CTD_human;ORPHANET
HgenePBX1C0343640African Burkitt's lymphoma2CTD_human
HgenePBX1C1968949Cakut2GENOMICS_ENGLAND
HgenePBX1C4721444Burkitt Leukemia2CTD_human
HgenePBX1C0013146Drug abuse1CTD_human
HgenePBX1C0013170Drug habituation1CTD_human
HgenePBX1C0013222Drug Use Disorders1CTD_human
HgenePBX1C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgenePBX1C0038580Substance Dependence1CTD_human
HgenePBX1C0038586Substance Use Disorders1CTD_human
HgenePBX1C0236969Substance-Related Disorders1CTD_human
HgenePBX1C0431692Bilateral renal hypoplasia1ORPHANET
HgenePBX1C0740858Substance abuse problem1CTD_human
HgenePBX1C1510472Drug Dependence1CTD_human
HgenePBX1C4316881Prescription Drug Abuse1CTD_human
HgenePBX1C4539968CONGENITAL ANOMALIES OF KIDNEY AND URINARY TRACT SYNDROME WITH OR WITHOUT HEARING LOSS, ABNORMAL EARS, OR DEVELOPMENTAL DELAY1GENOMICS_ENGLAND