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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:MLF2-TP53 (FusionGDB2 ID:54166)

Fusion Gene Summary for MLF2-TP53

check button Fusion gene summary
Fusion gene informationFusion gene name: MLF2-TP53
Fusion gene ID: 54166
HgeneTgene
Gene symbol

MLF2

TP53

Gene ID

8079

7157

Gene namemyeloid leukemia factor 2tumor protein p53
SynonymsNTN4BCC7|BMFS5|LFS1|P53|TRP53
Cytomap

12p13.31

17p13.1

Type of geneprotein-codingprotein-coding
Descriptionmyeloid leukemia factor 2myelodysplasia-myeloid leukemia factor 2cellular tumor antigen p53antigen NY-CO-13mutant tumor protein 53p53 tumor suppressorphosphoprotein p53transformation-related protein 53tumor protein 53tumor supressor p53
Modification date2020031320200329
UniProtAcc.

Q12888

Ensembl transtripts involved in fusion geneENST00000203630, ENST00000435120, 
ENST00000539187, ENST00000542154, 
ENST00000564181, 		ENST00000269305, 
ENST00000420246, ENST00000445888, 
ENST00000455263, ENST00000359597, 
ENST00000413465, ENST00000574684, 
Fusion gene scores* DoF score9 X 9 X 4=3247 X 7 X 4=196
# samples 99
** MAII scorelog2(9/324*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/196*10)=-1.12285674778553
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MLF2 [Title/Abstract] AND TP53 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMLF2(6857456)-TP53(7572728), # samples:1
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
TgeneTP53

GO:0000733

DNA strand renaturation

8183576

TgeneTP53

GO:0006355

regulation of transcription, DNA-templated

7587074

TgeneTP53

GO:0006974

cellular response to DNA damage stimulus

14744935|15710329|17938203

TgeneTP53

GO:0006978

DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator

16213212

TgeneTP53

GO:0006983

ER overload response

14744935

TgeneTP53

GO:0007050

cell cycle arrest

15149599

TgeneTP53

GO:0008104

protein localization

16507995

TgeneTP53

GO:0008285

negative regulation of cell proliferation

22783376

TgeneTP53

GO:0010628

positive regulation of gene expression

15314173|20332243

TgeneTP53

GO:0030330

DNA damage response, signal transduction by p53 class mediator

15149599

TgeneTP53

GO:0031497

chromatin assembly

16322561

TgeneTP53

GO:0034644

cellular response to UV

16213212|23629966

TgeneTP53

GO:0036003

positive regulation of transcription from RNA polymerase II promoter in response to stress

30089260

TgeneTP53

GO:0042149

cellular response to glucose starvation

14744935|21471221

TgeneTP53

GO:0042771

intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator

14654789|14744935|17403783

TgeneTP53

GO:0042981

regulation of apoptotic process

14744935

TgeneTP53

GO:0043065

positive regulation of apoptotic process

12667443|15565177|20959462

TgeneTP53

GO:0045892

negative regulation of transcription, DNA-templated

24051492

TgeneTP53

GO:0045893

positive regulation of transcription, DNA-templated

16322561|17403783|18549481|20378837

TgeneTP53

GO:0045899

positive regulation of RNA polymerase II transcriptional preinitiation complex assembly

24289924

TgeneTP53

GO:0045944

positive regulation of transcription by RNA polymerase II

11672523|17145718|17310983|17599062|18549481|20959462|24652652

TgeneTP53

GO:0051123

RNA polymerase II preinitiation complex assembly

24289924

TgeneTP53

GO:0051974

negative regulation of telomerase activity

10597287

TgeneTP53

GO:0065003

protein-containing complex assembly

12915590

TgeneTP53

GO:0071158

positive regulation of cell cycle arrest

15314173

TgeneTP53

GO:0071480

cellular response to gamma radiation

16213212

TgeneTP53

GO:0072331

signal transduction by p53 class mediator

15314173

TgeneTP53

GO:0072717

cellular response to actinomycin D

15314173

TgeneTP53

GO:0090200

positive regulation of release of cytochrome c from mitochondria

14963330

TgeneTP53

GO:0097252

oligodendrocyte apoptotic process

7720704

TgeneTP53

GO:1902895

positive regulation of pri-miRNA transcription by RNA polymerase II

20546595

TgeneTP53

GO:1903800

positive regulation of production of miRNAs involved in gene silencing by miRNA

26100857

TgeneTP53

GO:1990248

regulation of transcription from RNA polymerase II promoter in response to DNA damage

30089260


check buttonFusion gene breakpoints across MLF2 (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 TP53 (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
ChiTaRS5.0N/ABM991038MLF2chr12

6857456

+TP53chr17

7572728

-


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Fusion Gene ORF analysis for MLF2-TP53

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-3UTRENST00000203630ENST00000269305MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000203630ENST00000420246MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000203630ENST00000445888MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000203630ENST00000455263MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000435120ENST00000269305MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000435120ENST00000420246MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000435120ENST00000445888MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000435120ENST00000455263MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000539187ENST00000269305MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000539187ENST00000420246MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000539187ENST00000445888MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000539187ENST00000455263MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000542154ENST00000269305MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000542154ENST00000420246MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000542154ENST00000445888MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000542154ENST00000455263MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000564181ENST00000269305MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000564181ENST00000420246MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000564181ENST00000445888MLF2chr12

6857456

+TP53chr17

7572728

-
intron-3UTRENST00000564181ENST00000455263MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000203630ENST00000359597MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000203630ENST00000413465MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000203630ENST00000574684MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000435120ENST00000359597MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000435120ENST00000413465MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000435120ENST00000574684MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000539187ENST00000359597MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000539187ENST00000413465MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000539187ENST00000574684MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000542154ENST00000359597MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000542154ENST00000413465MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000542154ENST00000574684MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000564181ENST00000359597MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000564181ENST00000413465MLF2chr12

6857456

+TP53chr17

7572728

-
intron-intronENST00000564181ENST00000574684MLF2chr12

6857456

+TP53chr17

7572728

-

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 MLF2-TP53


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)

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 MLF2-TP53


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/:6857456/:7572728)
- 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
.TP53

Q12888

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}.FUNCTION: Double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis (PubMed:12364621, PubMed:22553214, PubMed:23333306, PubMed:17190600, PubMed:21144835, PubMed:27153538, PubMed:28241136). Plays a key role in the repair of double-strand DNA breaks (DSBs) in response to DNA damage by promoting non-homologous end joining (NHEJ)-mediated repair of DSBs and specifically counteracting the function of the homologous recombination (HR) repair protein BRCA1 (PubMed:22553214, PubMed:23727112, PubMed:23333306, PubMed:27153538). In response to DSBs, phosphorylation by ATM promotes interaction with RIF1 and dissociation from NUDT16L1/TIRR, leading to recruitment to DSBs sites (PubMed:28241136). Recruited to DSBs sites by recognizing and binding histone H2A monoubiquitinated at 'Lys-15' (H2AK15Ub) and histone H4 dimethylated at 'Lys-20' (H4K20me2), two histone marks that are present at DSBs sites (PubMed:23760478, PubMed:27153538, PubMed:28241136, PubMed:17190600). Required for immunoglobulin class-switch recombination (CSR) during antibody genesis, a process that involves the generation of DNA DSBs (PubMed:23345425). Participates in the repair and the orientation of the broken DNA ends during CSR (By similarity). In contrast, it is not required for classic NHEJ and V(D)J recombination (By similarity). Promotes NHEJ of dysfunctional telomeres via interaction with PAXIP1 (PubMed:23727112). {ECO:0000250|UniProtKB:P70399, ECO:0000269|PubMed:12364621, ECO:0000269|PubMed:17190600, ECO:0000269|PubMed:21144835, ECO:0000269|PubMed:22553214, ECO:0000269|PubMed:23333306, ECO:0000269|PubMed:23345425, ECO:0000269|PubMed:23727112, ECO:0000269|PubMed:23760478, ECO:0000269|PubMed:27153538, ECO:0000269|PubMed:28241136}.

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 MLF2-TP53


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 MLF2-TP53


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 MLF2-TP53


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 MLF2-TP53


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource