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Fusion Protein:WWOX-VAT1L

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: WWOX-VAT1L
	FusionPDB ID: 99500
	FusionGDB2.0 ID: 99500
		Hgene	Tgene
	Gene symbol	WWOX	VAT1L
	Gene ID	51741	57687
	Gene name	WW domain containing oxidoreductase	vesicle amine transport 1 like
	Synonyms	D16S432E\|EIEE28\|FOR\|FRA16D\|HHCMA56\|PRO0128\|SCAR12\|SDR41C1\|WOX1	-
	Cytomap	16q23.1-q23.2	16q23.1
	Type of gene	protein-coding	protein-coding
	Description	WW domain-containing oxidoreductaseWW domain-containing protein WWOXfragile site FRA16D oxidoreductaseshort chain dehydrogenase/reductase family 41C member 1	synaptic vesicle membrane protein VAT-1 homolog-likevesicle amine transport protein 1 homolog (T. californica)-likevesicle amine transport protein 1 homolog-like (T. californica)
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000565791, ENST00000355860, ENST00000402655, ENST00000406884, ENST00000408984, ENST00000539474, ENST00000566780, ENST00000569818,	ENST00000302536, ENST00000563850,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	26 X 26 X 8=5408	7 X 7 X 5=245
	# samples	31	9
	** MAII score	log2(31/5408*10)=-4.12475503100795 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/245*10)=-1.4447848426729 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: WWOX [Title/Abstract] AND VAT1L [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: WWOX [Title/Abstract] AND VAT1L [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	WWOX(78133782)-VAT1L(77850818), # samples:2
Anticipated loss of major functional domain due to fusion event.	WWOX-VAT1L 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. WWOX-VAT1L 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. WWOX-VAT1L 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. WWOX-VAT1L 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. WWOX-VAT1L seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. WWOX-VAT1L 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
Hgene	WWOX	GO:0030178	negative regulation of Wnt signaling pathway	19465938
Hgene	WWOX	GO:0071560	cellular response to transforming growth factor beta stimulus	19366691

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:78133782/chr16:77850818)
- 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 WWOX (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 VAT1L (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)
ENST00000566780	WWOX	chr16	78466649	+	ENST00000302536	VAT1L	chr16	78005747	+	4017	1422	366	1604	412
ENST00000408984	WWOX	chr16	78466649	+	ENST00000302536	VAT1L	chr16	78005747	+	3736	1141	85	1323	412
ENST00000566780	WWOX	chr16	78133782	+	ENST00000302536	VAT1L	chr16	77850818	+	3912	473	366	1499	377
ENST00000406884	WWOX	chr16	78133782	+	ENST00000302536	VAT1L	chr16	77850818	+	3671	232	125	1258	377
ENST00000539474	WWOX	chr16	78133782	+	ENST00000302536	VAT1L	chr16	77850818	+	3671	232	125	1258	377
ENST00000402655	WWOX	chr16	78133782	+	ENST00000302536	VAT1L	chr16	77850818	+	3671	232	125	1258	377
ENST00000408984	WWOX	chr16	78133782	+	ENST00000302536	VAT1L	chr16	77850818	+	3631	192	85	1218	377
ENST00000355860	WWOX	chr16	78133782	+	ENST00000302536	VAT1L	chr16	77850818	+	3646	207	100	1233	377
ENST00000566780	WWOX	chr16	78198186	-	ENST00000302536	VAT1L	chr16	78005747	+	3477	882	366	1064	232
ENST00000406884	WWOX	chr16	78198186	-	ENST00000302536	VAT1L	chr16	78005747	+	3236	641	125	823	232
ENST00000408984	WWOX	chr16	78198186	-	ENST00000302536	VAT1L	chr16	78005747	+	3196	601	85	783	232
ENST00000355860	WWOX	chr16	78198186	-	ENST00000302536	VAT1L	chr16	78005747	+	3211	616	100	798	232

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
ENST00000566780	ENST00000302536	WWOX	chr16	78466649	+	VAT1L	chr16	78005747	+	0.001582193	0.99841785
ENST00000408984	ENST00000302536	WWOX	chr16	78466649	+	VAT1L	chr16	78005747	+	0.001219762	0.9987802
ENST00000566780	ENST00000302536	WWOX	chr16	78133782	+	VAT1L	chr16	77850818	+	0.000401137	0.9995989
ENST00000406884	ENST00000302536	WWOX	chr16	78133782	+	VAT1L	chr16	77850818	+	0.000335286	0.99966466
ENST00000539474	ENST00000302536	WWOX	chr16	78133782	+	VAT1L	chr16	77850818	+	0.000335286	0.99966466
ENST00000402655	ENST00000302536	WWOX	chr16	78133782	+	VAT1L	chr16	77850818	+	0.000335286	0.99966466
ENST00000408984	ENST00000302536	WWOX	chr16	78133782	+	VAT1L	chr16	77850818	+	0.000321582	0.9996785
ENST00000355860	ENST00000302536	WWOX	chr16	78133782	+	VAT1L	chr16	77850818	+	0.000320877	0.9996791
ENST00000566780	ENST00000302536	WWOX	chr16	78198186	-	VAT1L	chr16	78005747	+	0.001187718	0.9988123
ENST00000406884	ENST00000302536	WWOX	chr16	78198186	-	VAT1L	chr16	78005747	+	0.000980372	0.9990196
ENST00000408984	ENST00000302536	WWOX	chr16	78198186	-	VAT1L	chr16	78005747	+	0.000927936	0.9990721
ENST00000355860	ENST00000302536	WWOX	chr16	78198186	-	VAT1L	chr16	78005747	+	0.000934041	0.99906594

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 WWOX-VAT1L

+/-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
WWOX	chr16	78133782	VAT1L	chr16	77850818	192	36	ERTTKDGWVYYANGLNFIDLMVRQGN
WWOX	chr16	78133782	VAT1L	chr16	77850818	207	36	ERTTKDGWVYYANGLNFIDLMVRQGN
WWOX	chr16	78133782	VAT1L	chr16	77850818	232	36	ERTTKDGWVYYANGLNFIDLMVRQGN
WWOX	chr16	78133782	VAT1L	chr16	77850818	473	36	ERTTKDGWVYYANGLNFIDLMVRQGN
WWOX	chr16	78198186	VAT1L	chr16	78005747	601	172	RASEAVSRILEEWVKEAMQRIHDRGN
WWOX	chr16	78198186	VAT1L	chr16	78005747	616	172	RASEAVSRILEEWVKEAMQRIHDRGN
WWOX	chr16	78198186	VAT1L	chr16	78005747	641	172	RASEAVSRILEEWVKEAMQRIHDRGN
WWOX	chr16	78198186	VAT1L	chr16	78005747	882	172	RASEAVSRILEEWVKEAMQRIHDRGN
WWOX	chr16	78466649	VAT1L	chr16	78005747	1141	352	LLFTLARPFTKSMVKEAMQRIHDRGN
WWOX	chr16	78466649	VAT1L	chr16	78005747	1422	352	LLFTLARPFTKSMVKEAMQRIHDRGN

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Potential FusionNeoAntigen Information of WWOX-VAT1L 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.

WWOX-VAT1L_78133782_77850818.msa
WWOX-VAT1L_78198186_78005747.msa
WWOX-VAT1L_78466649_78005747.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)
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-B15:18	VYYANGLNF	0.3321	0.6909	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:10	YYANGLNF	0.9793	0.9264	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:80	YYANGLNF	0.9765	0.8834	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:67	YYANGLNF	0.9765	0.8834	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:46	YYANGLNF	0.9549	0.7726	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C04:14	YYANGLNF	0.9549	0.7503	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-B15:21	VYYANGLNF	0.7715	0.9089	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C12:16	VYYANGLNF	0.489	0.9644	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:29	VYYANGLNF	0.4846	0.9371	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:80	VYYANGLNF	0.4489	0.9241	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:67	VYYANGLNF	0.4489	0.9241	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:19	VYYANGLNF	0.4475	0.6792	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:13	VYYANGLNF	0.4456	0.8968	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:10	VYYANGLNF	0.4322	0.9426	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:05	VYYANGLNF	0.4182	0.9454	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:27	VYYANGLNF	0.3737	0.9396	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:46	VYYANGLNF	0.3444	0.8406	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:95	VYYANGLNF	0.3166	0.6877	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:10	YYANGLNFI	0.1722	0.9158	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:05	YYANGLNFI	0.1666	0.9119	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:67	YYANGLNFI	0.1573	0.8583	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:80	YYANGLNFI	0.1573	0.8583	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C04:14	YYANGLNFI	0.149	0.6851	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C04:14	VYYANGLNF	0.144	0.7603	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:29	YYANGLNFI	0.142	0.8866	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:13	YYANGLNFI	0.1003	0.7972	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:27	YYANGLNFI	0.0904	0.8956	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C04:10	VYYANGLNF	0.0099	0.7378	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:17	YYANGLNF	0.977	0.9511	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:02	YYANGLNF	0.9765	0.8834	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C04:04	YYANGLNF	0.9459	0.778	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C14:03	YYANGLNF	0.9272	0.9575	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C14:02	YYANGLNF	0.9272	0.9575	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:06	YYANGLNF	0.8726	0.9855	9	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:22	VYYANGLNF	0.4806	0.7423	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C03:67	VYYANGLNF	0.4774	0.9781	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:02	VYYANGLNF	0.4489	0.9241	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:17	VYYANGLNF	0.3751	0.9563	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:01	VYYANGLNF	0.3599	0.679	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:02	VYYANGLNF	0.2114	0.995	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:17	VYYANGLNF	0.2114	0.995	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:04	VYYANGLNF	0.1785	0.8848	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C14:03	VYYANGLNF	0.1635	0.9558	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C14:02	VYYANGLNF	0.1635	0.9558	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:02	YYANGLNFI	0.1573	0.8583	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C03:67	YYANGLNFI	0.1467	0.9651	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C04:04	YYANGLNFI	0.1385	0.7346	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C07:04	YYANGLNFI	0.1024	0.8815	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C18:01	YYANGLNFI	0.0638	0.6444	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:17	YYANGLNFI	0.0564	0.9921	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:02	YYANGLNFI	0.0564	0.9921	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:06	YYANGLNFI	0.0519	0.9808	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C04:04	VYYANGLNF	0.0432	0.8697	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:08	VYYANGLNF	0.0248	0.9904	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:06	VYYANGLNF	0.0165	0.9851	8	17
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C14:03	YYANGLNFI	0.0152	0.9422	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C14:02	YYANGLNFI	0.0152	0.9422	9	18
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	HLA-C06:08	YYANGLNFI	0.0126	0.986	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:01	EEWVKEAM	0.9994	0.9661	10	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B27:05	SRILEEWVK	0.9988	0.9376	6	15
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:22	ILEEWVKEA	0.997	0.8918	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:30	ILEEWVKEA	0.9945	0.877	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:24	ILEEWVKEA	0.9945	0.877	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:67	ILEEWVKEA	0.9945	0.877	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:60	ILEEWVKEA	0.9943	0.8758	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:11	ILEEWVKEA	0.9942	0.8908	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:27	ILEEWVKEA	0.994	0.7977	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:01	LEEWVKEAM	0.992	0.9732	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:13	ILEEWVKEA	0.9907	0.8901	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:16	ILEEWVKEA	0.986	0.6539	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:38	ILEEWVKEA	0.9812	0.6649	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:19	ILEEWVKEA	0.9782	0.7834	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:29	ILEEWVKEA	0.8528	0.8743	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B39:13	LEEWVKEAM	0.6119	0.985	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B27:14	SRILEEWVK	0.9968	0.8801	6	15
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:01	ILEEWVKEA	0.9945	0.877	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B27:03	SRILEEWVK	0.9735	0.9475	6	15
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B39:08	LEEWVKEAM	0.7367	0.954	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B73:01	SRILEEWVKEA	0.9997	0.8564	6	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:07	EEWVKEAM	0.9994	0.9389	10	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:05	EEWVKEAM	0.9994	0.9661	10	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:04	EEWVKEAM	0.9993	0.9709	10	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:08	EEWVKEAM	0.9992	0.9555	10	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:06	EEWVKEAM	0.9992	0.9706	10	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:11	EEWVKEAM	0.9989	0.9503	10	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:03	EEWVKEAM	0.998	0.9625	10	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B40:04	LEEWVKEAM	0.9986	0.773	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B27:10	SRILEEWVK	0.9984	0.9178	6	15
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B27:08	SRILEEWVK	0.9983	0.9004	6	15
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-A02:03	ILEEWVKEA	0.9962	0.9287	8	17
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:04	LEEWVKEAM	0.9956	0.9765	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:06	LEEWVKEAM	0.9932	0.979	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:08	LEEWVKEAM	0.9926	0.9641	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:05	LEEWVKEAM	0.992	0.9732	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:03	LEEWVKEAM	0.9823	0.97	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B18:11	LEEWVKEAM	0.9094	0.978	9	18
WWOX-VAT1L	chr16	78198186	chr16	78005747	616	HLA-B41:03	LEEWVKEAM	0.6091	0.7821	9	18
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B08:09	RPFTKSMV	0.9969	0.6087	6	14
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B15:10	TKSMVKEAM	0.7532	0.5607	9	18
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B15:18	TKSMVKEAM	0.4445	0.775	9	18
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B15:37	TKSMVKEAM	0.3252	0.5933	9	18
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B27:05	ARPFTKSMVK	0.9993	0.8545	5	15
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-C12:04	MVKEAMQRI	0.9876	0.9948	12	21
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-C06:03	MVKEAMQRI	0.9871	0.9949	12	21
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B27:14	ARPFTKSMVK	0.9976	0.7757	5	15
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B27:03	ARPFTKSMVK	0.988	0.867	5	15
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-C16:01	KSMVKEAM	0.9952	0.9732	10	18
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-A68:02	MVKEAMQRI	0.9182	0.5223	12	21
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-A25:01	MVKEAMQRI	0.8128	0.8666	12	21
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-C06:08	ARPFTKSMV	0.7516	0.9854	5	14
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B15:09	TKSMVKEAM	0.7107	0.7676	9	18
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-C06:17	ARPFTKSMV	0.0421	0.9861	5	14
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-C06:02	ARPFTKSMV	0.0421	0.9861	5	14
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	HLA-B27:10	ARPFTKSMVK	0.9989	0.7992	5	15

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Potential FusionNeoAntigen Information of WWOX-VAT1L in HLA II

WWOX-VAT1L_78133782_77850818.msa
WWOX-VAT1L_78466649_78005747.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)
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1502	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1508	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1511	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1514	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1515	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1519	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1526	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1538	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1539	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1544	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78133782	chr16	77850818	207	DRB1-1547	KDGWVYYANGLNFID	4	19
WWOX-VAT1L	chr16	78466649	chr16	78005747	1141	DRB1-0902	ARPFTKSMVKEAMQR	5	20

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Fusion breakpoint peptide structures of WWOX-VAT1L

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
3244	GWVYYANGLNFIDL	WWOX	VAT1L	chr16	78133782	chr16	77850818	207

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
8081	RPFTKSMVKEAMQR	WWOX	VAT1L	chr16	78466649	chr16	78005747	1141

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
8956	SRILEEWVKEAMQR	WWOX	VAT1L	chr16	78198186	chr16	78005747	616

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of WWOX-VAT1L

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	3244	GWVYYANGLNFIDL	-8.85616	-8.96956
HLA-B14:02	3BVN	3244	GWVYYANGLNFIDL	-5.66423	-6.69953
HLA-B52:01	3W39	3244	GWVYYANGLNFIDL	-6.49489	-6.60829
HLA-B52:01	3W39	3244	GWVYYANGLNFIDL	-3.99785	-5.03315
HLA-A11:01	4UQ2	3244	GWVYYANGLNFIDL	-4.90759	-5.94289
HLA-A24:02	5HGA	3244	GWVYYANGLNFIDL	-7.27887	-7.39227
HLA-A24:02	5HGA	3244	GWVYYANGLNFIDL	-7.11524	-8.15054
HLA-B27:05	6PYJ	3244	GWVYYANGLNFIDL	-6.11615	-6.22955
HLA-B27:05	6PYJ	3244	GWVYYANGLNFIDL	-4.78818	-5.82348
HLA-B44:05	3DX8	3244	GWVYYANGLNFIDL	-7.22602	-7.33942
HLA-B44:05	3DX8	3244	GWVYYANGLNFIDL	-4.86671	-5.90201
HLA-B14:02	3BVN	8081	RPFTKSMVKEAMQR	-7.15543	-7.26883
HLA-B14:02	3BVN	8081	RPFTKSMVKEAMQR	-4.77435	-5.80965
HLA-B52:01	3W39	8081	RPFTKSMVKEAMQR	-6.80875	-6.92215
HLA-B52:01	3W39	8081	RPFTKSMVKEAMQR	-4.20386	-5.23916
HLA-A11:01	4UQ2	8081	RPFTKSMVKEAMQR	-7.5194	-8.5547
HLA-A11:01	4UQ2	8081	RPFTKSMVKEAMQR	-6.9601	-7.0735
HLA-A24:02	5HGA	8081	RPFTKSMVKEAMQR	-7.52403	-7.63743
HLA-A24:02	5HGA	8081	RPFTKSMVKEAMQR	-5.82433	-6.85963
HLA-B27:05	6PYJ	8081	RPFTKSMVKEAMQR	-3.28285	-4.31815
HLA-B44:05	3DX8	8081	RPFTKSMVKEAMQR	-5.91172	-6.94702
HLA-B44:05	3DX8	8081	RPFTKSMVKEAMQR	-4.24346	-4.35686
HLA-B14:02	3BVN	8956	SRILEEWVKEAMQR	-5.69703	-5.81043
HLA-B14:02	3BVN	8956	SRILEEWVKEAMQR	-3.30489	-4.34019
HLA-B52:01	3W39	8956	SRILEEWVKEAMQR	-6.15603	-6.26943
HLA-B52:01	3W39	8956	SRILEEWVKEAMQR	-2.53028	-3.56558
HLA-A11:01	4UQ2	8956	SRILEEWVKEAMQR	-8.02194	-8.13534
HLA-A11:01	4UQ2	8956	SRILEEWVKEAMQR	-4.77224	-5.80754
HLA-A24:02	5HGA	8956	SRILEEWVKEAMQR	-6.61646	-6.72986
HLA-A24:02	5HGA	8956	SRILEEWVKEAMQR	-3.90018	-4.93548
HLA-B27:05	6PYJ	8956	SRILEEWVKEAMQR	-1.07132	-2.10662
HLA-B27:03	6PZ5	8956	SRILEEWVKEAMQR	-5.01894	-5.13234
HLA-B27:03	6PZ5	8956	SRILEEWVKEAMQR	-3.96816	-5.00346
HLA-B44:05	3DX8	8956	SRILEEWVKEAMQR	-3.72692	-3.84032
HLA-B44:05	3DX8	8956	SRILEEWVKEAMQR	-3.6769	-4.7122
HLA-A02:01	6TDR	8956	SRILEEWVKEAMQR	-6.1456	-6.259
HLA-A02:01	6TDR	8956	SRILEEWVKEAMQR	-3.53626	-4.57156

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Vaccine Design for the FusionNeoAntigens of WWOX-VAT1L

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
WWOX-VAT1L	chr16	78133782	chr16	77850818	8	17	VYYANGLNF	GGTTTACTACGCCAATGGATTAAACTT
WWOX-VAT1L	chr16	78133782	chr16	77850818	9	17	YYANGLNF	TTACTACGCCAATGGATTAAACTT
WWOX-VAT1L	chr16	78133782	chr16	77850818	9	18	YYANGLNFI	TTACTACGCCAATGGATTAAACTTCAT
WWOX-VAT1L	chr16	78198186	chr16	78005747	10	18	EEWVKEAM	GAAGAATGGGTGAAGGAGGCCATG
WWOX-VAT1L	chr16	78198186	chr16	78005747	6	15	SRILEEWVK	TCACGCATTTTAGAAGAATGGGTGAAG
WWOX-VAT1L	chr16	78198186	chr16	78005747	6	17	SRILEEWVKEA	TCACGCATTTTAGAAGAATGGGTGAAGGAGGCC
WWOX-VAT1L	chr16	78198186	chr16	78005747	8	17	ILEEWVKEA	ATTTTAGAAGAATGGGTGAAGGAGGCC
WWOX-VAT1L	chr16	78198186	chr16	78005747	9	18	LEEWVKEAM	TTAGAAGAATGGGTGAAGGAGGCCATG
WWOX-VAT1L	chr16	78466649	chr16	78005747	10	18	KSMVKEAM	AAGTCCATGGTGAAGGAGGCCATG
WWOX-VAT1L	chr16	78466649	chr16	78005747	12	21	MVKEAMQRI	ATGGTGAAGGAGGCCATGCAGCGGATT
WWOX-VAT1L	chr16	78466649	chr16	78005747	5	14	ARPFTKSMV	GCGAGGCCTTTCACCAAGTCCATGGTG
WWOX-VAT1L	chr16	78466649	chr16	78005747	5	15	ARPFTKSMVK	GCGAGGCCTTTCACCAAGTCCATGGTGAAG
WWOX-VAT1L	chr16	78466649	chr16	78005747	6	14	RPFTKSMV	AGGCCTTTCACCAAGTCCATGGTG
WWOX-VAT1L	chr16	78466649	chr16	78005747	9	18	TKSMVKEAM	ACCAAGTCCATGGTGAAGGAGGCCATG

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
WWOX-VAT1L	chr16	78133782	chr16	77850818	4	19	KDGWVYYANGLNFID	CAAGGACGGCTGGGTTTACTACGCCAATGGATTAAACTTCATTGA
WWOX-VAT1L	chr16	78466649	chr16	78005747	5	20	ARPFTKSMVKEAMQR	GCGAGGCCTTTCACCAAGTCCATGGTGAAGGAGGCCATGCAGCGG

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Information of the samples that have these potential fusion neoantigens of WWOX-VAT1L

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
COAD	WWOX-VAT1L	chr16	78198186	ENST00000355860	chr16	78005747	ENST00000302536	TCGA-A6-4105-01A
STAD	WWOX-VAT1L	chr16	78133782	ENST00000355860	chr16	77850818	ENST00000302536	TCGA-CD-8535-01A
LUAD	WWOX-VAT1L	chr16	78466649	ENST00000408984	chr16	78005747	ENST00000302536	TCGA-44-7670-01A

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Potential target of CAR-T therapy development for WWOX-VAT1L

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

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Related Drugs to WWOX-VAT1L

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to WWOX-VAT1L

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)