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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: 32411

FusionGeneSummary for RUNX1_USP42

check button Fusion gene summary
Fusion gene informationFusion gene name: RUNX1_USP42
Fusion gene ID: 32411
HgeneTgene
Gene symbol

RUNX1

USP42

Gene ID

861

84132

Gene namerunt related transcription factor 1ubiquitin specific peptidase 42
SynonymsAML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha-
Cytomap

21q22.12

7p22.1

Type of geneprotein-codingprotein-coding
Descriptionrunt-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 2ubiquitin carboxyl-terminal hydrolase 42deubiquitinating enzyme 42ubiquitin specific protease 42ubiquitin thioesterase 42ubiquitin thiolesterase 42ubiquitin-specific-processing protease 42
Modification date2018052720180523
UniProtAcc

Q01196

Q9H9J4

Ensembl transtripts involved in fusion geneENST00000344691, ENST00000325074, 
ENST00000437180, ENST00000300305, 
ENST00000399240, ENST00000486278, 
ENST00000494829, ENST00000358356, 
ENST00000306177, 
Fusion gene scores* DoF score23 X 25 X 7=40254 X 4 X 3=48
# samples 535
** MAII scorelog2(53/4025*10)=-2.92492451843878
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/48*10)=0.0588936890535686
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RUNX1 [Title/Abstract] AND USP42 [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
HgeneRUNX1

GO:0030097

hemopoiesis

21873977

HgeneRUNX1

GO:0045893

positive regulation of transcription, DNA-templated

10207087|14970218

HgeneRUNX1

GO:0045944

positive regulation of transcription by RNA polymerase II

9199349|10207087|14970218|21873977

TgeneUSP42

GO:0016579

protein deubiquitination

14715245


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
ChiTaRS3.1FR727326RUNX1chr21

36167489

-USP42chr7

6150914

+
* 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-3CDSENST00000344691ENST00000306177RUNX1chr21

36167489

-USP42chr7

6150914

+
intron-3CDSENST00000325074ENST00000306177RUNX1chr21

36167489

-USP42chr7

6150914

+
intron-3CDSENST00000437180ENST00000306177RUNX1chr21

36167489

-USP42chr7

6150914

+
intron-3CDSENST00000300305ENST00000306177RUNX1chr21

36167489

-USP42chr7

6150914

+
intron-3CDSENST00000399240ENST00000306177RUNX1chr21

36167489

-USP42chr7

6150914

+
intron-3CDSENST00000486278ENST00000306177RUNX1chr21

36167489

-USP42chr7

6150914

+
intron-3CDSENST00000494829ENST00000306177RUNX1chr21

36167489

-USP42chr7

6150914

+
intron-3CDSENST00000358356ENST00000306177RUNX1chr21

36167489

-USP42chr7

6150914

+

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FusionProtFeatures for RUNX1_USP42


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RUNX1

Q01196

USP42

Q9H9J4

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 RUNX1_USP42


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 RUNX1_USP42


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 RUNX1_USP42


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 RUNX1_USP42


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRUNX1C0023467Leukemia, Myelocytic, Acute2CTD_human;HPO
HgeneRUNX1C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma2CTD_human
HgeneRUNX1C0003873Rheumatoid Arthritis1CTD_human
HgeneRUNX1C0017636Glioblastoma1CTD_human
HgeneRUNX1C0033578Prostatic Neoplasms1CTD_human
HgeneRUNX1C0349639Juvenile Myelomonocytic Leukemia1CTD_human
HgeneRUNX1C1832388Platelet Disorder, Familial, with Associated Myeloid Malignancy1CTD_human;ORPHANET;UNIPROT
HgeneRUNX1C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human