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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:CPNE1-DMD (FusionGDB2 ID:19010)

Fusion Gene Summary for CPNE1-DMD

Fusion gene summary

Fusion gene information	Fusion gene name: CPNE1-DMD
	Fusion gene ID: 19010
		Hgene	Tgene
	Gene symbol	CPNE1	DMD
	Gene ID	8904	1756
	Gene name	copine 1	dystrophin
	Synonyms	COPN1\|CPN1	BMD\|CMD3B\|DXS142\|DXS164\|DXS206\|DXS230\|DXS239\|DXS268\|DXS269\|DXS270\|DXS272\|MRX85
	Cytomap	20q11.22	Xp21.2-p21.1
	Type of gene	protein-coding	protein-coding
	Description	copine-1chromobindin 17copine I	dystrophin
	Modification date	20200320	20200329
	UniProtAcc	Q99829	P11532
	Ensembl transtripts involved in fusion gene	ENST00000475146, ENST00000317619, ENST00000352393, ENST00000397445, ENST00000317677, ENST00000397442, ENST00000397443, ENST00000397446,	ENST00000288447, ENST00000343523, ENST00000357033, ENST00000359836, ENST00000361471, ENST00000378677, ENST00000378680, ENST00000378702, ENST00000378707, ENST00000378723, ENST00000445312, ENST00000474231, ENST00000541735,
Fusion gene scores	* DoF score	18 X 14 X 7=1764	35 X 39 X 12=16380
	# samples	22	41
	** MAII score	log2(22/1764*10)=-3.00327513203286 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(41/16380*10)=-5.32016763702292 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CPNE1 [Title/Abstract] AND DMD [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CPNE1(34246852)-DMD(32408298), # 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	CPNE1	GO:0043392	negative regulation of DNA binding	18212740
Hgene	CPNE1	GO:0045666	positive regulation of neuron differentiation	23263657
Hgene	CPNE1	GO:0051897	positive regulation of protein kinase B signaling	23263657
Hgene	CPNE1	GO:1990138	neuron projection extension	23263657
Tgene	DMD	GO:0043043	peptide biosynthetic process	16000376

Fusion gene breakpoints across CPNE1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across DMD (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	LUAD	TCGA-75-5146-01A	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-

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Fusion Gene ORF analysis for CPNE1-DMD

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-intron	ENST00000475146	ENST00000288447	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000343523	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000357033	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000359836	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000361471	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000378677	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000378680	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000378702	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000378707	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000378723	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000445312	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000474231	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5CDS-intron	ENST00000475146	ENST00000541735	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000288447	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000343523	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000357033	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000359836	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000361471	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000378677	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000378680	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000378702	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000378707	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000378723	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000445312	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000474231	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000317619	ENST00000541735	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000288447	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000343523	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000357033	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000359836	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000361471	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000378677	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000378680	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000378702	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000378707	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000378723	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000445312	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000474231	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000352393	ENST00000541735	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000288447	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000343523	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000357033	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000359836	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000361471	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000378677	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000378680	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000378702	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000378707	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000378723	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000445312	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000474231	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
5UTR-intron	ENST00000397445	ENST00000541735	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000288447	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000343523	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000357033	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000359836	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000361471	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000378677	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000378680	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000378702	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000378707	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000378723	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000445312	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000474231	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000317677	ENST00000541735	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000288447	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000343523	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000357033	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000359836	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000361471	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000378677	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000378680	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000378702	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000378707	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000378723	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000445312	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000474231	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397442	ENST00000541735	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000288447	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000343523	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000357033	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000359836	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000361471	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000378677	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000378680	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000378702	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000378707	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000378723	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000445312	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000474231	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397443	ENST00000541735	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000288447	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000343523	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000357033	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000359836	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000361471	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000378677	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000378680	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000378702	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000378707	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000378723	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000445312	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000474231	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-
intron-intron	ENST00000397446	ENST00000541735	CPNE1	chr20	34246852	-	DMD	chrX	32408298	-

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for CPNE1-DMD

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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.

Distribution 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 CPNE1-DMD

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:34246852/:32408298)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
CPNE1 Q99829	DMD P11532
FUNCTION: Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes (PubMed:14674885). Involved in the TNF-alpha receptor signaling pathway in a calcium-dependent manner (PubMed:14674885). Exhibits calcium-dependent phospholipid binding properties (PubMed:9430674, PubMed:19539605). Plays a role in neuronal progenitor cell differentiation; induces neurite outgrowth via a AKT-dependent signaling cascade and calcium-independent manner (PubMed:23263657, PubMed:25450385). May recruit target proteins to the cell membrane in a calcium-dependent manner (PubMed:12522145). May function in membrane trafficking (PubMed:9430674). Involved in TNF-alpha-induced NF-kappa-B transcriptional repression by inducing endoprotease processing of the transcription factor NF-kappa-B p65/RELA subunit (PubMed:18212740). Also induces endoprotease processing of NF-kappa-B p50/NFKB1, p52/NFKB2, RELB and REL (PubMed:18212740). {ECO:0000269\|PubMed:12522145, ECO:0000269\|PubMed:14674885, ECO:0000269\|PubMed:18212740, ECO:0000269\|PubMed:19539605, ECO:0000269\|PubMed:23263657, ECO:0000269\|PubMed:25450385, ECO:0000269\|PubMed:9430674}.	FUNCTION: Anchors the extracellular matrix to the cytoskeleton via F-actin. Ligand for dystroglycan. Component of the dystrophin-associated glycoprotein complex which accumulates at the neuromuscular junction (NMJ) and at a variety of synapses in the peripheral and central nervous systems and has a structural function in stabilizing the sarcolemma. Also implicated in signaling events and synaptic transmission. {ECO:0000250\|UniProtKB:P11531, ECO:0000269\|PubMed:16710609}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for CPNE1-DMD

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 CPNE1-DMD

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for CPNE1-DMD

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for CPNE1-DMD

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source