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Fusion Protein:VIM-DES

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: VIM-DES
	FusionPDB ID: 98108
	FusionGDB2.0 ID: 98108
		Hgene	Tgene
	Gene symbol	VIM	DES
	Gene ID	7431	1674
	Gene name	vimentin	desmin
	Synonyms	-	CDCD3\|CMD1F\|CSM1\|CSM2\|LGMD1D\|LGMD1E\|LGMD2R
	Cytomap	10p13	2q35
	Type of gene	protein-coding	protein-coding
	Description	vimentinepididymis secretory sperm binding protein	desmincardiomyopathy, dilated 1F (autosomal dominant)epididymis secretory sperm binding proteinintermediate filament proteinmutant desmin p.K241E
	Modification date	20200327	20200329
	UniProtAcc	VMAC Main function of 5'-partner protein: 169	PPPDE2 Main function of 5'-partner protein: 168
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000485947, ENST00000224237, ENST00000544301,	ENST00000373960,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	38 X 18 X 13=8892	6 X 8 X 5=240
	# samples	42	9
	** MAII score	log2(42/8892*10)=-4.40404671536087 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/240*10)=-1.41503749927884 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: VIM [Title/Abstract] AND DES [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: VIM [Title/Abstract] AND DES [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	DES(220286282)-VIM(17277845), # samples:2 VIM(17275681)-DES(220285217), # samples:1 VIM(17271757)-DES(220283497), # samples:1
Anticipated loss of major functional domain due to fusion event.	DES-VIM seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. DES-VIM seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. VIM-DES seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. VIM-DES seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. VIM-DES seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. VIM-DES seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. VIM-DES seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. VIM-DES seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.

* 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr10:220286282/chr2:17277845)
- 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.

Retention analysis results 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, are available here.

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

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

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)

ENST00000544301

VIM

chr10

17275681

ENST00000373960

DES

chr2

220285217

2560

1133

413

1810

465

ENST00000224237

VIM

chr10

17275681

ENST00000373960

DES

chr2

220285217

2292

865

145

1542

465

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
ENST00000544301	ENST00000373960	VIM	chr10	17275681	+	DES	chr2	220285217	+	0.008785206	0.99121475
ENST00000224237	ENST00000373960	VIM	chr10	17275681	+	DES	chr2	220285217	+	0.008548084	0.99145186

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for VIM-DES

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
VIM	chr10	17275681	DES	chr2	220285217	1133	84	SSVPGVRLLQDSVDFSLADAINTEFK
VIM	chr10	17275681	DES	chr2	220285217	865	84	SSVPGVRLLQDSVDFSLADAINTEFK

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Potential FusionNeoAntigen Information of VIM-DES in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

VIM-DES_17275681_220285217.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:01	RLLQDSVDF	0.993	0.837	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:25	RLLQDSVDF	0.9462	0.9073	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:01	LQDSVDFSL	0.8663	0.8442	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:21	LQDSVDFSL	0.8563	0.5511	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:13	LQDSVDFSL	0.7753	0.8352	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B38:01	LQDSVDFSL	0.6802	0.9025	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B38:02	LQDSVDFSL	0.6633	0.9102	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B13:02	LQDSVDFSL	0.6218	0.5977	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B13:01	LQDSVDFSL	0.56	0.9562	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B13:01	RLLQDSVDF	0.0778	0.9307	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:22	LLQDSVDFSL	0.9966	0.6156	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:30	LLQDSVDFSL	0.993	0.5756	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:24	LLQDSVDFSL	0.993	0.5756	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:67	LLQDSVDFSL	0.993	0.5756	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:60	LLQDSVDFSL	0.9927	0.5747	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:11	LLQDSVDFSL	0.9924	0.5782	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:27	LLQDSVDFSL	0.9882	0.6057	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:04	LLQDSVDFSL	0.9847	0.6407	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:19	LLQDSVDFSL	0.9566	0.5199	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:29	LLQDSVDFSL	0.9001	0.5741	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:20	LLQDSVDFSL	0.8864	0.5859	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:60	RLLQDSVDFSL	0.9983	0.5388	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:67	RLLQDSVDFSL	0.9982	0.5167	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:24	RLLQDSVDFSL	0.9982	0.5167	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:30	RLLQDSVDFSL	0.9982	0.5167	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:04	RLLQDSVDFSL	0.9962	0.5899	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:29	RLLQDSVDFSL	0.9503	0.5192	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:20	RLLQDSVDFSL	0.9459	0.5225	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B48:01	RLLQDSVDFSL	0.9023	0.52	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B13:01	RLLQDSVDFSL	0.749	0.9796	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C05:09	LQDSVDFSL	0.9998	0.951	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C04:10	LQDSVDFSL	0.9998	0.7294	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C04:07	LQDSVDFSL	0.9997	0.7633	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C08:15	LQDSVDFSL	0.9996	0.9753	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C04:06	LQDSVDFSL	0.9738	0.7023	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C08:03	LQDSVDFSL	0.9563	0.9855	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C08:13	LQDSVDFSL	0.9522	0.9625	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C08:04	LQDSVDFSL	0.9522	0.9625	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C04:14	LQDSVDFSL	0.9131	0.7128	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:09	LQDSVDFSL	0.8609	0.5256	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:07	LQDSVDFSL	0.8479	0.5547	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:08	LQDSVDFSL	0.8101	0.901	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:05	LQDSVDFSL	0.7073	0.8116	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:05	RLLQDSVDF	0.5802	0.8643	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:01	LLQDSVDFSL	0.993	0.5756	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:07	LLQDSVDFSL	0.9929	0.6507	7	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:01	RLLQDSVDFSL	0.9982	0.5167	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:08	RLLQDSVDFSL	0.8057	0.9484	6	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C04:03	LQDSVDFSL	0.9998	0.8453	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C05:01	LQDSVDFSL	0.9998	0.951	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C04:01	LQDSVDFSL	0.9997	0.7633	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C08:02	LQDSVDFSL	0.9996	0.9753	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C18:01	LQDSVDFSL	0.9995	0.8359	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:33	RLLQDSVDF	0.993	0.837	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:34	RLLQDSVDF	0.993	0.837	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:125	RLLQDSVDF	0.993	0.837	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A32:01	RLLQDSVDF	0.9817	0.9311	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-C08:01	LQDSVDFSL	0.9563	0.9855	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:39	RLLQDSVDF	0.9527	0.8029	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:02	LQDSVDFSL	0.8766	0.8503	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:31	LQDSVDFSL	0.8739	0.8457	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:14	LQDSVDFSL	0.8579	0.5046	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-A02:06	LQDSVDFSL	0.8563	0.5511	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B39:11	LQDSVDFSL	0.7795	0.8591	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B38:05	LQDSVDFSL	0.6802	0.9025	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:73	LQDSVDFSL	0.5811	0.7402	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:20	RLLQDSVDF	0.5796	0.9034	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B35:13	LQDSVDFSL	0.574	0.8826	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B35:28	RLLQDSVDF	0.5157	0.9058	6	15
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B15:09	LQDSVDFSL	0.4482	0.7192	8	17
VIM-DES	chr10	17275681	chr2	220285217	865	HLA-B40:21	RLLQDSVDFSL	0.7505	0.513	6	17

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Potential FusionNeoAntigen Information of VIM-DES in HLA II

VIM-DES_17275681_220285217.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0113	SVDFSLADAINTEFK	11	26
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0117	SVDFSLADAINTEFK	11	26
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0121	SVDFSLADAINTEFK	11	26
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0129	SVDFSLADAINTEFK	11	26
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0411	SVPGVRLLQDSVDFS	1	16
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0411	VPGVRLLQDSVDFSL	2	17
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0411	SSVPGVRLLQDSVDF	0	15
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0467	SVPGVRLLQDSVDFS	1	16
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0467	VPGVRLLQDSVDFSL	2	17
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0491	SVPGVRLLQDSVDFS	1	16
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0491	VPGVRLLQDSVDFSL	2	17
VIM-DES	chr10	17275681	chr2	220285217	865	DRB1-0491	SSVPGVRLLQDSVDF	0	15
VIM-DES	chr10	17275681	chr2	220285217	865	DRB4-0104	GVRLLQDSVDFSLAD	4	19

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Fusion breakpoint peptide structures of VIM-DES

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
8016	RLLQDSVDFSLADA	VIM	DES	chr10	17275681	chr2	220285217	865

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of VIM-DES

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	8016	RLLQDSVDFSLADA	-7.9962	-8.1096
HLA-B14:02	3BVN	8016	RLLQDSVDFSLADA	-5.70842	-6.74372
HLA-B52:01	3W39	8016	RLLQDSVDFSLADA	-6.83737	-6.95077
HLA-B52:01	3W39	8016	RLLQDSVDFSLADA	-4.4836	-5.5189
HLA-A11:01	4UQ2	8016	RLLQDSVDFSLADA	-10.0067	-10.1201
HLA-A11:01	4UQ2	8016	RLLQDSVDFSLADA	-9.03915	-10.0745
HLA-A24:02	5HGA	8016	RLLQDSVDFSLADA	-6.56204	-6.67544
HLA-A24:02	5HGA	8016	RLLQDSVDFSLADA	-5.42271	-6.45801
HLA-B44:05	3DX8	8016	RLLQDSVDFSLADA	-7.85648	-8.89178
HLA-B44:05	3DX8	8016	RLLQDSVDFSLADA	-5.3978	-5.5112
HLA-A02:01	6TDR	8016	RLLQDSVDFSLADA	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of VIM-DES

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
VIM-DES	chr10	17275681	chr2	220285217	6	15	RLLQDSVDF	TTGAAGAAACTCCACGAAGAGGAGATC
VIM-DES	chr10	17275681	chr2	220285217	6	17	RLLQDSVDFSL	TTGAAGAAACTCCACGAAGAGGAGATCCGTGAG
VIM-DES	chr10	17275681	chr2	220285217	7	17	LLQDSVDFSL	AAGAAACTCCACGAAGAGGAGATCCGTGAG
VIM-DES	chr10	17275681	chr2	220285217	8	17	LQDSVDFSL	AAACTCCACGAAGAGGAGATCCGTGAG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
VIM-DES	chr10	17275681	chr2	220285217	0	15	SSVPGVRLLQDSVDF	CAAGAAGAGATTGCCTTTTTGAAGAAACTCCACGAAGAGGAGATC
VIM-DES	chr10	17275681	chr2	220285217	1	16	SVPGVRLLQDSVDFS	GAAGAGATTGCCTTTTTGAAGAAACTCCACGAAGAGGAGATCCGT
VIM-DES	chr10	17275681	chr2	220285217	11	26	SVDFSLADAINTEFK	GAAGAGGAGATCCGTGAGTTGCAGGCTCAGCTTCAGGAACAGCAG
VIM-DES	chr10	17275681	chr2	220285217	2	17	VPGVRLLQDSVDFSL	GAGATTGCCTTTTTGAAGAAACTCCACGAAGAGGAGATCCGTGAG
VIM-DES	chr10	17275681	chr2	220285217	4	19	GVRLLQDSVDFSLAD	GCCTTTTTGAAGAAACTCCACGAAGAGGAGATCCGTGAGTTGCAG

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Information of the samples that have these potential fusion neoantigens of VIM-DES

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
GBM	VIM-DES	chr10	17275681	ENST00000224237	chr2	220285217	ENST00000373960	TCGA-06-0644-01A

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Potential target of CAR-T therapy development for VIM-DES

Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

Top

Related Drugs to VIM-DES

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to VIM-DES

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)