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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: 41134

FusionGeneSummary for USP42_RUNX1

check button Fusion gene summary
Fusion gene informationFusion gene name: USP42_RUNX1
Fusion gene ID: 41134
HgeneTgene
Gene symbol

USP42

RUNX1

Gene ID

84132

861

Gene nameubiquitin specific peptidase 42runt related transcription factor 1
Synonyms-AML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha
Cytomap

7p22.1

21q22.12

Type of geneprotein-codingprotein-coding
Descriptionubiquitin carboxyl-terminal hydrolase 42deubiquitinating enzyme 42ubiquitin specific protease 42ubiquitin thioesterase 42ubiquitin thiolesterase 42ubiquitin-specific-processing protease 42runt-related transcription factor 1AML1-EVI-1 fusion proteinPEA2-alpha BPEBP2-alpha BSL3-3 enhancer factor 1 alpha B subunitSL3/AKV core-binding factor alpha B subunitacute myeloid leukemia 1 proteincore-binding factor, runt domain, alpha subunit 2
Modification date2018052320180527
UniProtAcc

Q9H9J4

Q01196

Ensembl transtripts involved in fusion geneENST00000306177, ENST00000344691, 
ENST00000325074, ENST00000437180, 
ENST00000300305, ENST00000399240, 
ENST00000486278, ENST00000494829, 
ENST00000358356, 
Fusion gene scores* DoF score4 X 4 X 2=3217 X 29 X 7=3451
# samples 533
** MAII scorelog2(5/32*10)=0.643856189774725
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(33/3451*10)=-3.3864765441897
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: USP42 [Title/Abstract] AND RUNX1 [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
HgeneUSP42

GO:0016579

protein deubiquitination

14715245

TgeneRUNX1

GO:0030097

hemopoiesis

21873977

TgeneRUNX1

GO:0045893

positive regulation of transcription, DNA-templated

10207087|14970218

TgeneRUNX1

GO:0045944

positive regulation of transcription by RNA polymerase II

9199349|10207087|14970218|21873977


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
ChiTaRS3.1FR727327USP42chr7

6151080

+RUNX1chr21

36167584

-
* 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
intron-intronENST00000306177ENST00000344691USP42chr7

6151080

+RUNX1chr21

36167584

-
intron-intronENST00000306177ENST00000325074USP42chr7

6151080

+RUNX1chr21

36167584

-
intron-intronENST00000306177ENST00000437180USP42chr7

6151080

+RUNX1chr21

36167584

-
intron-intronENST00000306177ENST00000300305USP42chr7

6151080

+RUNX1chr21

36167584

-
intron-intronENST00000306177ENST00000399240USP42chr7

6151080

+RUNX1chr21

36167584

-
intron-intronENST00000306177ENST00000486278USP42chr7

6151080

+RUNX1chr21

36167584

-
intron-intronENST00000306177ENST00000494829USP42chr7

6151080

+RUNX1chr21

36167584

-
intron-intronENST00000306177ENST00000358356USP42chr7

6151080

+RUNX1chr21

36167584

-

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FusionProtFeatures for USP42_RUNX1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
USP42

Q9H9J4

RUNX1

Q01196

Deubiquitinating enzyme which may play an important roleduring spermatogenesis. {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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FusionGeneSequence for USP42_RUNX1


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 USP42_RUNX1


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 USP42_RUNX1


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 USP42_RUNX1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneRUNX1C0023467Leukemia, Myelocytic, Acute2CTD_human;HPO
TgeneRUNX1C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma2CTD_human
TgeneRUNX1C0003873Rheumatoid Arthritis1CTD_human
TgeneRUNX1C0017636Glioblastoma1CTD_human
TgeneRUNX1C0033578Prostatic Neoplasms1CTD_human
TgeneRUNX1C0349639Juvenile Myelomonocytic Leukemia1CTD_human
TgeneRUNX1C1832388Platelet Disorder, Familial, with Associated Myeloid Malignancy1CTD_human;ORPHANET;UNIPROT
TgeneRUNX1C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human