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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:RUNX1-PRDX4 (FusionGDB2 ID:HG861TG10549)

Fusion Gene Summary for RUNX1-PRDX4

check button Fusion gene summary
Fusion gene informationFusion gene name: RUNX1-PRDX4
Fusion gene ID: hg861tg10549
HgeneTgene
Gene symbol

RUNX1

PRDX4

Gene ID

861

10549

Gene nameRUNX family transcription factor 1peroxiredoxin 4
SynonymsAML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alphaAOE37-2|AOE372|HEL-S-97n|PRX-4
Cytomap('RUNX1')('PRDX4')

21q22.12

Xp22.11

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 2peroxiredoxin-4antioxidant enzyme AOE372epididymis secretory sperm binding protein Li 97nperoxiredoxin IVprx-IVthioredoxin peroxidase (antioxidant enzyme)thioredoxin peroxidase AO372thioredoxin-dependent peroxide reductase A0372
Modification date2020032220200313
UniProtAcc

Q01196

.
Ensembl transtripts involved in fusion geneENST00000300305, ENST00000325074, 
ENST00000344691, ENST00000358356, 
ENST00000399240, ENST00000437180, 
ENST00000486278, ENST00000494829, 
Fusion gene scores* DoF score46 X 68 X 13=406645 X 7 X 3=105
# samples 896
** MAII scorelog2(89/40664*10)=-5.51380298959468
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/105*10)=-0.807354922057604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RUNX1 [Title/Abstract] AND PRDX4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint
Anticipated loss of major functional domain due to fusion event.
* 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



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
ChimerKB4..RUNX1chr21

36231875

-PRDX4chrX

36231875

+


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Fusion Gene ORF analysis for RUNX1-PRDX4

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-intronENST00000300305ENST00000379331RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000300305ENST00000379341RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000300305ENST00000495599RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000325074ENST00000379331RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000325074ENST00000379341RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000325074ENST00000495599RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000344691ENST00000379331RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000344691ENST00000379341RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000344691ENST00000495599RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000358356ENST00000379331RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000358356ENST00000379341RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000358356ENST00000495599RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000399240ENST00000379331RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000399240ENST00000379341RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000399240ENST00000495599RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000437180ENST00000379331RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000437180ENST00000379341RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000437180ENST00000495599RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000486278ENST00000379331RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000486278ENST00000379341RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000486278ENST00000495599RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000494829ENST00000379331RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000494829ENST00000379341RUNX1chr21

36231875

-PRDX4chrX

36231875

+
intron-intronENST00000494829ENST00000495599RUNX1chr21

36231875

-PRDX4chrX

36231875

+

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 RUNX1-PRDX4


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)


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Fusion Protein Features for RUNX1-PRDX4


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:/:)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

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

Q01196

.
FUNCTION: Forms the heterodimeric complex core-binding factor (CBF) with CBFB. RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'-TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX. The heterodimers bind to the core site of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, LCK, IL3 and GM-CSF promoters (Probable). Essential for the development of normal hematopoiesis (PubMed:17431401). Acts synergistically with ELF4 to transactivate the IL-3 promoter and with ELF2 to transactivate the BLK promoter (PubMed:10207087, PubMed:14970218). Inhibits KAT6B-dependent transcriptional activation (By similarity). Involved in lineage commitment of immature T cell precursors. CBF complexes repress ZBTB7B transcription factor during cytotoxic (CD8+) T cell development. They bind to RUNX-binding sequence within the ZBTB7B locus acting as transcriptional silencer and allowing for cytotoxic T cell differentiation. CBF complexes binding to the transcriptional silencer is essential for recruitment of nuclear protein complexes that catalyze epigenetic modifications to establish epigenetic ZBTB7B silencing (By similarity). Controls the anergy and suppressive function of regulatory T-cells (Treg) by associating with FOXP3. Activates the expression of IL2 and IFNG and down-regulates the expression of TNFRSF18, IL2RA and CTLA4, in conventional T-cells (PubMed:17377532). Positively regulates the expression of RORC in T-helper 17 cells (By similarity). {ECO:0000250|UniProtKB:Q03347, ECO:0000269|PubMed:10207087, ECO:0000269|PubMed:11965546, ECO:0000269|PubMed:14970218, ECO:0000269|PubMed:17377532, ECO:0000269|PubMed:17431401, ECO:0000305}.; FUNCTION: Isoform AML-1G shows higher binding activities for target genes and binds TCR-beta-E2 and RAG-1 target site with threefold higher affinity than other isoforms. It is less effective in the context of neutrophil terminal differentiation. {ECO:0000250|UniProtKB:Q03347}.; FUNCTION: Isoform AML-1L interferes with the transactivation activity of RUNX1. {ECO:0000269|PubMed:9199349}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {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 RUNX1-PRDX4


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 RUNX1-PRDX4


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 RUNX1-PRDX4


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 RUNX1-PRDX4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRUNX1C1832388Platelet Disorder, Familial, with Associated Myeloid Malignancy11CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneRUNX1C0023467Leukemia, Myelocytic, Acute4CGI;CTD_human;GENOMICS_ENGLAND
HgeneRUNX1C0026998Acute Myeloid Leukemia, M13CTD_human
HgeneRUNX1C1879321Acute Myeloid Leukemia (AML-M2)3CTD_human
HgeneRUNX1C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma2CTD_human
HgeneRUNX1C0003873Rheumatoid Arthritis1CTD_human
HgeneRUNX1C0006413Burkitt Lymphoma1ORPHANET
HgeneRUNX1C0017636Glioblastoma1CTD_human
HgeneRUNX1C0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
HgeneRUNX1C0023453L2 Acute Lymphoblastic Leukemia1CTD_human
HgeneRUNX1C0023473Myeloid Leukemia, Chronic1ORPHANET
HgeneRUNX1C0033578Prostatic Neoplasms1CTD_human
HgeneRUNX1C0040034Thrombocytopenia1GENOMICS_ENGLAND
HgeneRUNX1C0334588Giant Cell Glioblastoma1CTD_human
HgeneRUNX1C0349639Juvenile Myelomonocytic Leukemia1CTD_human
HgeneRUNX1C0376358Malignant neoplasm of prostate1CTD_human
HgeneRUNX1C1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
HgeneRUNX1C1621958Glioblastoma Multiforme1CTD_human
HgeneRUNX1C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human
HgeneRUNX1C2713368Hematopoetic Myelodysplasia1CTD_human
HgeneRUNX1C3463824MYELODYSPLASTIC SYNDROME1CTD_human
TgeneC0020456Hyperglycemia1CTD_human
TgeneC0079744Diffuse Large B-Cell Lymphoma1CTD_human
TgeneC0162820Dermatitis, Allergic Contact1CTD_human
TgeneC0235874Disease Exacerbation1CTD_human
TgeneC0271650Impaired glucose tolerance1CTD_human
TgeneC1855520Hyperglycemia, Postprandial1CTD_human