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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:NRF1-MTMR1 (FusionGDB2 ID:60262)

Fusion Gene Summary for NRF1-MTMR1

check button Fusion gene summary
Fusion gene informationFusion gene name: NRF1-MTMR1
Fusion gene ID: 60262
HgeneTgene
Gene symbol

NRF1

MTMR1

Gene ID

4899

8776

Gene namenuclear respiratory factor 1myotubularin related protein 1
SynonymsALPHA-PAL-
Cytomap

7q32.2

Xq28

Type of geneprotein-codingprotein-coding
Descriptionnuclear respiratory factor 1alpha palindromic-binding proteinmyotubularin-related protein 1phosphatidylinositol-3,5-bisphosphate 3-phosphatasephosphatidylinositol-3-phosphate phosphatase
Modification date2020032920200313
UniProtAcc.

Q8NCE2

Ensembl transtripts involved in fusion geneENST00000477428, ENST00000223190, 
ENST00000311967, ENST00000353868, 
ENST00000393230, ENST00000393232, 
ENST00000539636, ENST00000393231, 
ENST00000541925, ENST00000370390, 
ENST00000445323, ENST00000451863, 
ENST00000538506, ENST00000542156, 
ENST00000544228, 
Fusion gene scores* DoF score14 X 9 X 8=10088 X 8 X 4=256
# samples 169
** MAII scorelog2(16/1008*10)=-2.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/256*10)=-1.50814690367033
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NRF1 [Title/Abstract] AND MTMR1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNRF1(129251665)-MTMR1(149919202), # samples:3
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
TgeneMTMR1

GO:0046856

phosphatidylinositol dephosphorylation

11733541|27018598

TgeneMTMR1

GO:0060304

regulation of phosphatidylinositol dephosphorylation

16787938


check buttonFusion gene breakpoints across NRF1 (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 MTMR1 (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
ChimerDB4LUSCTCGA-33-4547-01ANRF1chr7

129251665

-MTMR1chrX

149919202

+
ChimerDB4LUSCTCGA-33-4547-01ANRF1chr7

129251665

+MTMR1chrX

149919202

+
ChimerDB4LUSCTCGA-33-4547NRF1chr7

129251665

+MTMR1chrX

149919202

+
ChimerDB4LUSCTCGA-33-4547NRF1chr7

129270009

+MTMR1chrX

149919202

+


Top

Fusion Gene ORF analysis for NRF1-MTMR1

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-3CDSENST00000477428ENST00000541925NRF1chr7

129251665

+MTMR1chrX

149919202

+
3UTR-3CDSENST00000477428ENST00000541925NRF1chr7

129270009

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000370390NRF1chr7

129251665

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000370390NRF1chr7

129270009

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000445323NRF1chr7

129251665

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000445323NRF1chr7

129270009

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000451863NRF1chr7

129251665

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000451863NRF1chr7

129270009

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000538506NRF1chr7

129251665

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000538506NRF1chr7

129270009

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000542156NRF1chr7

129251665

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000542156NRF1chr7

129270009

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000544228NRF1chr7

129251665

+MTMR1chrX

149919202

+
3UTR-intronENST00000477428ENST00000544228NRF1chr7

129270009

+MTMR1chrX

149919202

+
5UTR-3CDSENST00000223190ENST00000541925NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-3CDSENST00000311967ENST00000541925NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-3CDSENST00000353868ENST00000541925NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-3CDSENST00000393230ENST00000541925NRF1chr7

129270009

+MTMR1chrX

149919202

+
5UTR-3CDSENST00000393232ENST00000541925NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-3CDSENST00000539636ENST00000541925NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000223190ENST00000370390NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000223190ENST00000445323NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000223190ENST00000451863NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000223190ENST00000538506NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000223190ENST00000542156NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000223190ENST00000544228NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000311967ENST00000370390NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000311967ENST00000445323NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000311967ENST00000451863NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000311967ENST00000538506NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000311967ENST00000542156NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000311967ENST00000544228NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000353868ENST00000370390NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000353868ENST00000445323NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000353868ENST00000451863NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000353868ENST00000538506NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000353868ENST00000542156NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000353868ENST00000544228NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000393230ENST00000370390NRF1chr7

129270009

+MTMR1chrX

149919202

+
5UTR-intronENST00000393230ENST00000445323NRF1chr7

129270009

+MTMR1chrX

149919202

+
5UTR-intronENST00000393230ENST00000451863NRF1chr7

129270009

+MTMR1chrX

149919202

+
5UTR-intronENST00000393230ENST00000538506NRF1chr7

129270009

+MTMR1chrX

149919202

+
5UTR-intronENST00000393230ENST00000542156NRF1chr7

129270009

+MTMR1chrX

149919202

+
5UTR-intronENST00000393230ENST00000544228NRF1chr7

129270009

+MTMR1chrX

149919202

+
5UTR-intronENST00000393232ENST00000370390NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000393232ENST00000445323NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000393232ENST00000451863NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000393232ENST00000538506NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000393232ENST00000542156NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000393232ENST00000544228NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000539636ENST00000370390NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000539636ENST00000445323NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000539636ENST00000451863NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000539636ENST00000538506NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000539636ENST00000542156NRF1chr7

129251665

+MTMR1chrX

149919202

+
5UTR-intronENST00000539636ENST00000544228NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-3CDSENST00000223190ENST00000541925NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-3CDSENST00000311967ENST00000541925NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-3CDSENST00000353868ENST00000541925NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-3CDSENST00000393230ENST00000541925NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-3CDSENST00000393231ENST00000541925NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-3CDSENST00000393231ENST00000541925NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-3CDSENST00000393232ENST00000541925NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-3CDSENST00000539636ENST00000541925NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000223190ENST00000370390NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000223190ENST00000445323NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000223190ENST00000451863NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000223190ENST00000538506NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000223190ENST00000542156NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000223190ENST00000544228NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000311967ENST00000370390NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000311967ENST00000445323NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000311967ENST00000451863NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000311967ENST00000538506NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000311967ENST00000542156NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000311967ENST00000544228NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000353868ENST00000370390NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000353868ENST00000445323NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000353868ENST00000451863NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000353868ENST00000538506NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000353868ENST00000542156NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000353868ENST00000544228NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393230ENST00000370390NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393230ENST00000445323NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393230ENST00000451863NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393230ENST00000538506NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393230ENST00000542156NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393230ENST00000544228NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000370390NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000370390NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000445323NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000445323NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000451863NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000451863NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000538506NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000538506NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000542156NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000542156NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000544228NRF1chr7

129251665

+MTMR1chrX

149919202

+
intron-intronENST00000393231ENST00000544228NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393232ENST00000370390NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393232ENST00000445323NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393232ENST00000451863NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393232ENST00000538506NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393232ENST00000542156NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000393232ENST00000544228NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000539636ENST00000370390NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000539636ENST00000445323NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000539636ENST00000451863NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000539636ENST00000538506NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000539636ENST00000542156NRF1chr7

129270009

+MTMR1chrX

149919202

+
intron-intronENST00000539636ENST00000544228NRF1chr7

129270009

+MTMR1chrX

149919202

+

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 NRF1-MTMR1


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)
NRF1chr7129270009+MTMR1chrX149919201+0.73608740.26391262
NRF1chr7129251665+MTMR1chrX149919201+0.0001889930.999811
NRF1chr7129251665+MTMR1chrX149919201+0.0001889930.999811
NRF1chr7129270009+MTMR1chrX149919201+0.73608740.26391262
NRF1chr7129251665+MTMR1chrX149919201+0.0001889930.999811
NRF1chr7129251665+MTMR1chrX149919201+0.0001889930.999811

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.
genomic feature of top 1%

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Fusion Protein Features for NRF1-MTMR1


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/:129251665/:149919202)
- 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
.MTMR1

Q8NCE2

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: Lipid phosphatase which efficiently dephosphorylates phosphatidylinositol 3-phosphate (PtdIns3P) and PtdIns(3,5)P2; inactive toward PtdIns4P, PtdIns(3,4)P2, PtdIns(4,5)P2 and PtdIns(3,4,5)P3. {ECO:0000269|PubMed:17008356}.

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 NRF1-MTMR1


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 NRF1-MTMR1


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 NRF1-MTMR1


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 NRF1-MTMR1


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