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Fusion Protein:PTK7-DLK2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTK7-DLK2
	FusionPDB ID: 70072
	FusionGDB2.0 ID: 70072
		Hgene	Tgene
	Gene symbol	PTK7	DLK2
	Gene ID	5754	65989
	Gene name	protein tyrosine kinase 7 (inactive)	delta like non-canonical Notch ligand 2
	Synonyms	CCK-4\|CCK4	DLK-2\|EGFL9
	Cytomap	6p21.1	6p21.1
	Type of gene	protein-coding	protein-coding
	Description	inactive tyrosine-protein kinase 7PTK7 protein tyrosine kinase 7colon carcinoma kinase 4pseudo tyrosine kinase receptor 7tyrosine-protein kinase-like 7	protein delta homolog 2EGF-like protein 9EGF-like-domain, multiple 9delta-like 2 homologepidermal growth factor-like protein 9
	Modification date	20200322	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000230419, ENST00000345201, ENST00000349241, ENST00000352931, ENST00000471863, ENST00000476760, ENST00000481273,	ENST00000357338, ENST00000372485, ENST00000372488, ENST00000414245,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 6 X 10=900	1 X 1 X 1=1
	# samples	14	1
	** MAII score	log2(14/900*10)=-2.68449817427207 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(1/1*10)=3.32192809488736
Fusion gene context	PubMed: PTK7 [Title/Abstract] AND DLK2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PTK7 [Title/Abstract] AND DLK2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTK7(43044305)-DLK2(43422212), # samples:3
Anticipated loss of major functional domain due to fusion event.	PTK7-DLK2 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. PTK7-DLK2 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. PTK7-DLK2 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. PTK7-DLK2 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.

* 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
Tgene	DLK2	GO:0045746	negative regulation of Notch signaling pathway	25093684

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:43044305/chr6:43422212)
- 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 PTK7 (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 DLK2 (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)
ENST00000230419	PTK7	chr6	43044305	+	ENST00000372485	DLK2	chr6	43422212	-	1545	300	8	1357	449
ENST00000230419	PTK7	chr6	43044305	+	ENST00000372488	DLK2	chr6	43422212	-	1563	300	8	1375	455
ENST00000230419	PTK7	chr6	43044305	+	ENST00000414245	DLK2	chr6	43422212	-	1543	300	8	1357	449
ENST00000230419	PTK7	chr6	43044305	+	ENST00000357338	DLK2	chr6	43422212	-	1561	300	8	1375	455
ENST00000349241	PTK7	chr6	43044305	+	ENST00000372485	DLK2	chr6	43422212	-	1471	226	99	1283	394
ENST00000349241	PTK7	chr6	43044305	+	ENST00000372488	DLK2	chr6	43422212	-	1489	226	99	1301	400
ENST00000349241	PTK7	chr6	43044305	+	ENST00000414245	DLK2	chr6	43422212	-	1469	226	99	1283	394
ENST00000349241	PTK7	chr6	43044305	+	ENST00000357338	DLK2	chr6	43422212	-	1487	226	99	1301	400
ENST00000345201	PTK7	chr6	43044305	+	ENST00000372485	DLK2	chr6	43422212	-	1471	226	99	1283	394
ENST00000345201	PTK7	chr6	43044305	+	ENST00000372488	DLK2	chr6	43422212	-	1489	226	99	1301	400
ENST00000345201	PTK7	chr6	43044305	+	ENST00000414245	DLK2	chr6	43422212	-	1469	226	99	1283	394
ENST00000345201	PTK7	chr6	43044305	+	ENST00000357338	DLK2	chr6	43422212	-	1487	226	99	1301	400
ENST00000352931	PTK7	chr6	43044305	+	ENST00000372485	DLK2	chr6	43422212	-	1471	226	99	1283	394
ENST00000352931	PTK7	chr6	43044305	+	ENST00000372488	DLK2	chr6	43422212	-	1489	226	99	1301	400
ENST00000352931	PTK7	chr6	43044305	+	ENST00000414245	DLK2	chr6	43422212	-	1469	226	99	1283	394
ENST00000352931	PTK7	chr6	43044305	+	ENST00000357338	DLK2	chr6	43422212	-	1487	226	99	1301	400
ENST00000476760	PTK7	chr6	43044305	+	ENST00000372485	DLK2	chr6	43422212	-	1506	261	8	1318	436
ENST00000476760	PTK7	chr6	43044305	+	ENST00000372488	DLK2	chr6	43422212	-	1524	261	8	1336	442
ENST00000476760	PTK7	chr6	43044305	+	ENST00000414245	DLK2	chr6	43422212	-	1504	261	8	1318	436
ENST00000476760	PTK7	chr6	43044305	+	ENST00000357338	DLK2	chr6	43422212	-	1522	261	8	1336	442
ENST00000471863	PTK7	chr6	43044305	+	ENST00000372485	DLK2	chr6	43422212	-	1474	229	102	1286	394
ENST00000471863	PTK7	chr6	43044305	+	ENST00000372488	DLK2	chr6	43422212	-	1492	229	102	1304	400
ENST00000471863	PTK7	chr6	43044305	+	ENST00000414245	DLK2	chr6	43422212	-	1472	229	102	1286	394
ENST00000471863	PTK7	chr6	43044305	+	ENST00000357338	DLK2	chr6	43422212	-	1490	229	102	1304	400

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
ENST00000230419	ENST00000372485	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.20128618	0.79871374
ENST00000230419	ENST00000372488	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.19730015	0.8026998
ENST00000230419	ENST00000414245	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.2011336	0.79886645
ENST00000230419	ENST00000357338	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.19724692	0.80275315
ENST00000349241	ENST00000372485	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.2125762	0.78742385
ENST00000349241	ENST00000372488	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.2129385	0.7870615
ENST00000349241	ENST00000414245	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21242967	0.7875703
ENST00000349241	ENST00000357338	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21289577	0.7871043
ENST00000345201	ENST00000372485	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.2125762	0.78742385
ENST00000345201	ENST00000372488	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.2129385	0.7870615
ENST00000345201	ENST00000414245	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21242967	0.7875703
ENST00000345201	ENST00000357338	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21289577	0.7871043
ENST00000352931	ENST00000372485	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.2125762	0.78742385
ENST00000352931	ENST00000372488	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.2129385	0.7870615
ENST00000352931	ENST00000414245	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21242967	0.7875703
ENST00000352931	ENST00000357338	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21289577	0.7871043
ENST00000476760	ENST00000372485	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21655904	0.78344095
ENST00000476760	ENST00000372488	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21561494	0.7843851
ENST00000476760	ENST00000414245	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21637309	0.78362685
ENST00000476760	ENST00000357338	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21538135	0.7846186
ENST00000471863	ENST00000372485	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.212368	0.7876319
ENST00000471863	ENST00000372488	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21100186	0.7889982
ENST00000471863	ENST00000414245	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21229182	0.78770816
ENST00000471863	ENST00000357338	PTK7	chr6	43044305	+	DLK2	chr6	43422212	-	0.21088313	0.78911686

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 PTK7-DLK2

+/-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
PTK7	chr6	43044305	DLK2	chr6	43422212	226	30	GAARGSPARPRRLPLLSVLLLPLLGA
PTK7	chr6	43044305	DLK2	chr6	43422212	229	30	GAARGSPARPRRLPLLSVLLLPLLGA
PTK7	chr6	43044305	DLK2	chr6	43422212	261	72	GAARGSPARPRRLPLLSVLLLPLLGA

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Potential FusionNeoAntigen Information of PTK7-DLK2 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.

PTK7-DLK2_43044305_43422212.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)
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:07	RRLPLLSV	1	0.5917	10	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:04	RRLPLLSV	1	0.8097	10	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:02	RPRRLPLL	0.9998	0.684	8	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:03	LPLLSVLL	0.9898	0.8911	12	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:02	LPLLSVLL	0.9669	0.9528	12	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:04	LPLLSVLL	0.9669	0.9528	12	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:05	RRLPLLSVL	0.9999	0.8582	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:02	RRLPLLSVL	0.9999	0.644	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:07	RRLPLLSVL	0.9999	0.5668	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:04	RRLPLLSVL	0.9999	0.8507	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:24	RRLPLLSVL	0.9976	0.728	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:07	ARPRRLPLL	0.9975	0.5446	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:06	RRLPLLSVL	0.9968	0.9425	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:01	RRLPLLSVL	0.9944	0.9658	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B14:01	RRLPLLSVL	0.9881	0.9567	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B14:02	RRLPLLSVL	0.9881	0.9567	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B38:01	RRLPLLSVL	0.9858	0.9855	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:03	LPLLSVLLL	0.9853	0.8573	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B38:02	RRLPLLSVL	0.9832	0.9866	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B14:02	ARPRRLPLL	0.9811	0.8899	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B14:01	ARPRRLPLL	0.9811	0.8899	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:01	LPLLSVLLL	0.9573	0.8073	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-A02:04	RLPLLSVLL	0.9523	0.6883	11	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-A02:17	RLPLLSVLL	0.9508	0.6445	11	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:04	LPLLSVLLL	0.9301	0.9425	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:02	LPLLSVLLL	0.9301	0.9425	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:05	LPLLSVLLL	0.9233	0.5043	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B15:37	RRLPLLSVL	0.5371	0.7527	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:10	RRLPLLSVL	0.3268	0.6359	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:05	RRLPLLSVLL	0.9999	0.7284	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:07	RRLPLLSVLL	0.9999	0.5289	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:04	RRLPLLSVLL	0.9999	0.779	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:02	SPARPRRLPL	0.9994	0.6943	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:10	SPARPRRLPL	0.9993	0.7226	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:02	RPRRLPLLSV	0.9984	0.7715	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:05	RPRRLPLLSV	0.9984	0.7107	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B08:09	SPARPRRLPL	0.9492	0.5444	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:02	RPRRLPLLSVL	1	0.7419	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:04	RRLPLLSVLLL	1	0.7154	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:05	RRLPLLSVLLL	1	0.6219	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:07	RRLPLLSVLLL	1	0.5258	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:05	RPRRLPLLSVL	0.9999	0.6311	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:02	SPARPRRLPLL	0.9999	0.7397	5	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:05	SPARPRRLPLL	0.9999	0.5163	5	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:02	GSPARPRRLPL	0.9828	0.7146	4	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:04	RPRRLPLLSVL	0.9819	0.7985	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:02	RPRRLPLLSVL	0.9752	0.5097	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:05	RPRRLPLLSVL	0.9707	0.7642	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:14	RRLPLLSV	1	0.7947	10	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:12	RPRRLPLL	0.9987	0.8314	8	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:04	RPRRLPLL	0.998	0.6629	8	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C01:17	RLPLLSVL	0.9878	0.9662	11	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:12	LPLLSVLL	0.9669	0.9528	12	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C01:30	RLPLLSVL	0.9394	0.9777	11	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:10	LPLLSVLL	0.8537	0.9608	12	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:14	RRLPLLSVL	0.9999	0.8067	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:05	RRLPLLSVL	0.9994	0.9606	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:95	RRLPLLSVL	0.9994	0.7647	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:13	RRLPLLSVL	0.9987	0.8964	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:27	RRLPLLSVL	0.9984	0.9511	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:29	RRLPLLSVL	0.9982	0.9543	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:03	RRLPLLSVL	0.9975	0.8736	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:09	RRLPLLSVL	0.9952	0.8923	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:12	RRLPLLSVL	0.9933	0.9686	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:46	RRLPLLSVL	0.9881	0.8757	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:95	ARPRRLPLL	0.9767	0.6945	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:05	ARPRRLPLL	0.9738	0.9307	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:19	RRLPLLSVL	0.9737	0.7657	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B51:07	LPLLSVLLL	0.9705	0.7882	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:10	RRLPLLSVL	0.9664	0.9588	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:05	RRLPLLSVL	0.9659	0.9561	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:80	RRLPLLSVL	0.9649	0.9482	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:67	RRLPLLSVL	0.9649	0.9482	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:27	ARPRRLPLL	0.9633	0.9451	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-A02:07	RLPLLSVLL	0.9557	0.5534	11	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B73:01	RRLPLLSVL	0.9502	0.8464	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:46	ARPRRLPLL	0.9318	0.9122	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:12	LPLLSVLLL	0.9301	0.9425	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:29	ARPRRLPLL	0.9236	0.9401	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:19	ARPRRLPLL	0.9036	0.7889	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B42:02	LPLLSVLLL	0.9026	0.917	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:13	ARPRRLPLL	0.9001	0.9389	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:80	ARPRRLPLL	0.9	0.9642	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:67	ARPRRLPLL	0.9	0.9642	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:04	PARPRRLPL	0.8947	0.5749	6	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:10	ARPRRLPLL	0.8724	0.9583	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B42:01	LPLLSVLLL	0.8551	0.9126	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B14:03	RRLPLLSVL	0.7264	0.927	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:10	LPLLSVLLL	0.7048	0.9501	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C01:17	RLPLLSVLL	0.617	0.9619	11	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C12:16	RRLPLLSVL	0.389	0.977	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C01:30	RLPLLSVLL	0.3778	0.9731	11	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C12:16	ARPRRLPLL	0.2209	0.9656	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:14	RRLPLLSVLL	0.9999	0.6936	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:05	RRLPLLSVLL	0.9992	0.9578	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:95	RRLPLLSVLL	0.999	0.7245	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:03	RRLPLLSVLL	0.9987	0.7552	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:12	SPARPRRLPL	0.9966	0.8068	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:12	RPRRLPLLSV	0.9947	0.8828	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:04	SPARPRRLPL	0.9873	0.6063	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:04	RPRRLPLLSV	0.9868	0.7407	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B42:02	RPRRLPLLSV	0.9588	0.6047	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B42:01	RPRRLPLLSV	0.9464	0.6016	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:10	SPARPRRLPL	0.6676	0.8707	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:14	RRLPLLSVLLL	1	0.6245	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:05	RRLPLLSVLLL	0.9998	0.9577	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:95	RRLPLLSVLLL	0.9997	0.7091	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:12	RPRRLPLLSVL	0.9997	0.8784	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:03	RRLPLLSVLLL	0.9997	0.6577	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:12	SPARPRRLPLL	0.999	0.8353	5	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:04	SPARPRRLPLL	0.9923	0.6619	5	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:04	RPRRLPLLSVL	0.9805	0.7312	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:04	GSPARPRRLPL	0.9798	0.6589	4	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:14	RPRRLPLLSVL	0.9725	0.7217	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B42:01	RPRRLPLLSVL	0.9661	0.6821	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B42:02	RPRRLPLLSVL	0.9649	0.6801	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:03	RPRRLPLLSVL	0.5137	0.7814	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:08	RRLPLLSV	1	0.8075	10	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:10	RRLPLLSV	1	0.8821	10	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:09	RRLPLLSV	1	0.8131	10	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:06	RRLPLLSV	1	0.7919	10	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:22	RPRRLPLL	0.9998	0.684	8	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:09	RPRRLPLL	0.9998	0.6806	8	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B78:02	LPLLSVLL	0.9989	0.6322	12	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C01:02	RLPLLSVL	0.9905	0.9659	11	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C01:03	RLPLLSVL	0.9873	0.9331	11	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:09	LPLLSVLL	0.9669	0.9528	12	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B67:01	LPLLSVLL	0.9258	0.8972	12	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:26	RPRRLPLL	0.8409	0.5449	8	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:10	RRLPLLSVL	0.9999	0.9073	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:09	RRLPLLSVL	0.9999	0.833	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:06	RRLPLLSVL	0.9999	0.8312	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:08	RRLPLLSVL	0.9999	0.797	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:01	RRLPLLSVL	0.9996	0.7078	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:06	ARPRRLPLL	0.9989	0.8338	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:17	RRLPLLSVL	0.9972	0.9741	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:09	ARPRRLPLL	0.9967	0.8058	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:02	RRLPLLSVL	0.9945	0.9742	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B39:31	RRLPLLSVL	0.9943	0.9669	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C06:08	RRLPLLSVL	0.989	0.9931	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B38:05	RRLPLLSVL	0.9858	0.9855	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:13	LPLLSVLLL	0.9839	0.8682	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:04	RRLPLLSVL	0.9826	0.8815	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:01	ARPRRLPLL	0.9807	0.6719	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B78:02	LPLLSVLLL	0.9769	0.6393	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:22	RRLPLLSVL	0.9765	0.8199	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:02	RRLPLLSVL	0.9649	0.9482	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:77	LPLLSVLLL	0.9573	0.8073	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:23	LPLLSVLLL	0.956	0.8144	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:30	LPLLSVLLL	0.9339	0.6517	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:17	LPLLSVLLL	0.9339	0.6517	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:17	ARPRRLPLL	0.9303	0.9679	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:09	LPLLSVLLL	0.9301	0.9425	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B35:24	LPLLSVLLL	0.9193	0.7989	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:02	ARPRRLPLL	0.9	0.9642	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C06:08	ARPRRLPLL	0.8735	0.9945	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:22	ARPRRLPLL	0.8419	0.7434	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B67:01	LPLLSVLLL	0.7497	0.8904	12	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:04	ARPRRLPLL	0.6827	0.9465	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C01:03	RLPLLSVLL	0.6675	0.9493	11	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C06:06	RRLPLLSVL	0.667	0.9957	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C03:67	RRLPLLSVL	0.6646	0.9676	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C01:02	RLPLLSVLL	0.6398	0.9613	11	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C06:17	RRLPLLSVL	0.5341	0.9974	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C06:02	RRLPLLSVL	0.5341	0.9974	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B15:68	RRLPLLSVL	0.5238	0.6983	10	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:26	RPRRLPLLS	0.4028	0.5618	8	17
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C06:06	ARPRRLPLL	0.38	0.9933	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C06:17	ARPRRLPLL	0.2152	0.9944	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C06:02	ARPRRLPLL	0.2152	0.9944	7	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:10	RRLPLLSVLL	0.9999	0.8619	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:06	RRLPLLSVLL	0.9999	0.7811	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:08	RRLPLLSVLL	0.9999	0.6263	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:09	RRLPLLSVLL	0.9998	0.6908	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:22	SPARPRRLPL	0.9994	0.6943	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:09	SPARPRRLPL	0.9993	0.6572	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:01	RRLPLLSVLL	0.9992	0.6713	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:22	RPRRLPLLSV	0.9984	0.7715	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:09	RPRRLPLLSV	0.998	0.7602	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:22	RRLPLLSVLL	0.9948	0.7873	10	20
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B08:12	SPARPRRLPL	0.914	0.5712	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:26	SPARPRRLPL	0.8321	0.5163	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:26	RPRRLPLLSV	0.8283	0.57	8	18
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B67:01	SPARPRRLPL	0.6035	0.7648	5	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:08	RRLPLLSVLLL	1	0.5094	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:06	RRLPLLSVLLL	1	0.7246	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:10	RRLPLLSVLLL	1	0.7948	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:22	RPRRLPLLSVL	1	0.7419	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:09	RPRRLPLLSVL	0.9999	0.7281	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:09	RRLPLLSVLLL	0.9999	0.6091	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:22	SPARPRRLPLL	0.9999	0.7397	5	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:09	SPARPRRLPLL	0.9999	0.7236	5	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-C07:01	RRLPLLSVLLL	0.9998	0.6626	10	21
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:10	RPRRLPLLSVL	0.9829	0.8927	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:22	GSPARPRRLPL	0.9828	0.7146	4	15
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:08	RPRRLPLLSVL	0.9685	0.6567	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:06	RPRRLPLLSVL	0.9618	0.8192	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:26	SPARPRRLPLL	0.9534	0.5168	5	16
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B27:09	RPRRLPLLSVL	0.9246	0.7284	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B07:26	RPRRLPLLSVL	0.8994	0.5657	8	19
PTK7-DLK2	chr6	43044305	chr6	43422212	226	HLA-B67:01	RPRRLPLLSVL	0.651	0.7991	8	19

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Potential FusionNeoAntigen Information of PTK7-DLK2 in HLA II

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)

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Fusion breakpoint peptide structures of PTK7-DLK2

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
6505	PARPRRLPLLSVLL	PTK7	DLK2	chr6	43044305	chr6	43422212	226

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTK7-DLK2

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	6505	PARPRRLPLLSVLL	-7.15543	-7.26883
HLA-B14:02	3BVN	6505	PARPRRLPLLSVLL	-4.77435	-5.80965
HLA-B52:01	3W39	6505	PARPRRLPLLSVLL	-6.80875	-6.92215
HLA-B52:01	3W39	6505	PARPRRLPLLSVLL	-4.20386	-5.23916
HLA-A11:01	4UQ2	6505	PARPRRLPLLSVLL	-7.5194	-8.5547
HLA-A11:01	4UQ2	6505	PARPRRLPLLSVLL	-6.9601	-7.0735
HLA-A24:02	5HGA	6505	PARPRRLPLLSVLL	-7.52403	-7.63743
HLA-A24:02	5HGA	6505	PARPRRLPLLSVLL	-5.82433	-6.85963
HLA-B27:05	6PYJ	6505	PARPRRLPLLSVLL	-3.28285	-4.31815
HLA-B44:05	3DX8	6505	PARPRRLPLLSVLL	-5.91172	-6.94702
HLA-B44:05	3DX8	6505	PARPRRLPLLSVLL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of PTK7-DLK2

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
PTK7-DLK2	chr6	43044305	chr6	43422212	10	18	RRLPLLSV	TGCTGGGCGCCGATGACTGCAGCT
PTK7-DLK2	chr6	43044305	chr6	43422212	10	19	RRLPLLSVL	TGCTGGGCGCCGATGACTGCAGCTCCC
PTK7-DLK2	chr6	43044305	chr6	43422212	10	20	RRLPLLSVLL	TGCTGGGCGCCGATGACTGCAGCTCCCACT
PTK7-DLK2	chr6	43044305	chr6	43422212	10	21	RRLPLLSVLLL	TGCTGGGCGCCGATGACTGCAGCTCCCACTGTG
PTK7-DLK2	chr6	43044305	chr6	43422212	11	19	RLPLLSVL	TGGGCGCCGATGACTGCAGCTCCC
PTK7-DLK2	chr6	43044305	chr6	43422212	11	20	RLPLLSVLL	TGGGCGCCGATGACTGCAGCTCCCACT
PTK7-DLK2	chr6	43044305	chr6	43422212	12	20	LPLLSVLL	GCGCCGATGACTGCAGCTCCCACT
PTK7-DLK2	chr6	43044305	chr6	43422212	12	21	LPLLSVLLL	GCGCCGATGACTGCAGCTCCCACTGTG
PTK7-DLK2	chr6	43044305	chr6	43422212	4	15	GSPARPRRLPL	GCGTCCTGCTGCTGCCGCTGCTGGGCGCCGATG
PTK7-DLK2	chr6	43044305	chr6	43422212	5	15	SPARPRRLPL	TCCTGCTGCTGCCGCTGCTGGGCGCCGATG
PTK7-DLK2	chr6	43044305	chr6	43422212	5	16	SPARPRRLPLL	TCCTGCTGCTGCCGCTGCTGGGCGCCGATGACT
PTK7-DLK2	chr6	43044305	chr6	43422212	6	15	PARPRRLPL	TGCTGCTGCCGCTGCTGGGCGCCGATG
PTK7-DLK2	chr6	43044305	chr6	43422212	7	16	ARPRRLPLL	TGCTGCCGCTGCTGGGCGCCGATGACT
PTK7-DLK2	chr6	43044305	chr6	43422212	8	16	RPRRLPLL	TGCCGCTGCTGGGCGCCGATGACT
PTK7-DLK2	chr6	43044305	chr6	43422212	8	17	RPRRLPLLS	TGCCGCTGCTGGGCGCCGATGACTGCA
PTK7-DLK2	chr6	43044305	chr6	43422212	8	18	RPRRLPLLSV	TGCCGCTGCTGGGCGCCGATGACTGCAGCT
PTK7-DLK2	chr6	43044305	chr6	43422212	8	19	RPRRLPLLSVL	TGCCGCTGCTGGGCGCCGATGACTGCAGCTCCC

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

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Information of the samples that have these potential fusion neoantigens of PTK7-DLK2

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
LUAD	PTK7-DLK2	chr6	43044305	ENST00000345201	chr6	43422212	ENST00000357338	TCGA-05-4420-01A

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Potential target of CAR-T therapy development for PTK7-DLK2

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

Tgene

DLK2

chr6:43044305

chr6:43422212

ENST00000357338

307_327

384.0

Transmembrane

Helical

Tgene

DLK2

chr6:43044305

chr6:43422212

ENST00000372488

307_327

384.0

Transmembrane

Helical

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 PTK7-DLK2

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 PTK7-DLK2

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)