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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 22692

FusionGeneSummary for MSX1_MSX1

check button Fusion gene summary
Fusion gene informationFusion gene name: MSX1_MSX1
Fusion gene ID: 22692
HgeneTgene
Gene symbol

MSX1

MSX1

Gene ID

4487

4487

Gene namemsh homeobox 1msh homeobox 1
SynonymsECTD3|HOX7|HYD1|STHAG1ECTD3|HOX7|HYD1|STHAG1
Cytomap

4p16.2

4p16.2

Type of geneprotein-codingprotein-coding
Descriptionhomeobox protein MSX-1homeobox 7homeobox protein Hox-7msh homeo box 1msh homeobox 1-like proteinmsh homeobox homolog 1homeobox protein MSX-1homeobox 7homeobox protein Hox-7msh homeo box 1msh homeobox 1-like proteinmsh homeobox homolog 1
Modification date2018051920180519
UniProtAcc

P28360

P28360

Ensembl transtripts involved in fusion geneENST00000382723, ENST00000468421, 
ENST00000382723, ENST00000468421, 
Fusion gene scores* DoF score1 X 1 X 1=11 X 1 X 1=1
# samples 11
** MAII scorelog2(1/1*10)=3.32192809488736log2(1/1*10)=3.32192809488736
Context

PubMed: MSX1 [Title/Abstract] AND MSX1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneMSX1

GO:0000902

cell morphogenesis

15705871

HgeneMSX1

GO:0030308

negative regulation of cell growth

15705871

HgeneMSX1

GO:0034504

protein localization to nucleus

15705871

HgeneMSX1

GO:0050821

protein stabilization

15705871

HgeneMSX1

GO:1902255

positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator

15705871

TgeneMSX1

GO:0000902

cell morphogenesis

15705871

TgeneMSX1

GO:0030308

negative regulation of cell growth

15705871

TgeneMSX1

GO:0034504

protein localization to nucleus

15705871

TgeneMSX1

GO:0050821

protein stabilization

15705871

TgeneMSX1

GO:1902255

positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator

15705871


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1BU624994MSX1chr4

4865416

-MSX1chr4

4865033

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
3UTR-3UTRENST00000382723ENST00000382723MSX1chr4

4865416

-MSX1chr4

4865033

+
3UTR-intronENST00000382723ENST00000468421MSX1chr4

4865416

-MSX1chr4

4865033

+
intron-3UTRENST00000468421ENST00000382723MSX1chr4

4865416

-MSX1chr4

4865033

+
intron-intronENST00000468421ENST00000468421MSX1chr4

4865416

-MSX1chr4

4865033

+

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FusionProtFeatures for MSX1_MSX1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MSX1

P28360

MSX1

P28360

Acts as a transcriptional repressor. May play a role inlimb-pattern formation. Acts in cranofacial development andspecifically in odontogenesis. Expression in the developing nailbed mesenchyme is important for nail plate thickness andintegrity. {ECO:0000269|PubMed:11369996,ECO:0000269|PubMed:12807959}. Acts as a transcriptional repressor. May play a role inlimb-pattern formation. Acts in cranofacial development andspecifically in odontogenesis. Expression in the developing nailbed mesenchyme is important for nail plate thickness andintegrity. {ECO:0000269|PubMed:11369996,ECO:0000269|PubMed:12807959}.

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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FusionGeneSequence for MSX1_MSX1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for MSX1_MSX1


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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RelatedDrugs for MSX1_MSX1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for MSX1_MSX1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMSX1C0376634Craniofacial Abnormalities4CTD_human
HgeneMSX1C0008925Cleft Palate3CTD_human;HPO
HgeneMSX1C1837210OROFACIAL CLEFT 52CTD_human;UNIPROT
HgeneMSX1C3489529Tooth Agenesis, Familial2UNIPROT
HgeneMSX1C0038356Stomach Neoplasms1CTD_human
HgeneMSX1C0040427Tooth Abnormalities1CTD_human
HgeneMSX1C1956097Wolf-Hirschhorn Syndrome1CTD_human
TgeneMSX1C0376634Craniofacial Abnormalities4CTD_human
TgeneMSX1C0008925Cleft Palate3CTD_human;HPO
TgeneMSX1C1837210OROFACIAL CLEFT 52CTD_human;UNIPROT
TgeneMSX1C3489529Tooth Agenesis, Familial2UNIPROT
TgeneMSX1C0038356Stomach Neoplasms1CTD_human
TgeneMSX1C0040427Tooth Abnormalities1CTD_human
TgeneMSX1C1956097Wolf-Hirschhorn Syndrome1CTD_human