Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:DDR1-PAK1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: DDR1-PAK1
	FusionPDB ID: 21845
	FusionGDB2.0 ID: 21845
		Hgene	Tgene
	Gene symbol	DDR1	PAK1
	Gene ID	780	5585
	Gene name	discoidin domain receptor tyrosine kinase 1	protein kinase N1
	Synonyms	CAK\|CD167\|DDR\|EDDR1\|HGK2\|MCK10\|NEP\|NTRK4\|PTK3\|PTK3A\|RTK6\|TRKE	DBK\|PAK-1\|PAK1\|PKN\|PKN-ALPHA\|PRK1\|PRKCL1
	Cytomap	6p21.33	19p13.12
	Type of gene	protein-coding	protein-coding
	Description	epithelial discoidin domain-containing receptor 1CD167 antigen-like family member APTK3A protein tyrosine kinase 3Acell adhesion kinasemammary carcinoma kinase 10neuroepithelial tyrosine kinaseneurotrophic tyrosine kinase, receptor, type 4protein-t	serine/threonine-protein kinase N1protease-activated kinase 1protein kinase C-like 1protein kinase C-like PKNprotein kinase C-related kinase 1protein kinase PKN-alphaserine-threonine kinase Nserine/threonine protein kinase N
	Modification date	20200329	20200329
	UniProtAcc	Q08345 Main function of 5'-partner protein: FUNCTION: Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell attachment to the extracellular matrix, remodeling of the extracellular matrix, cell migration, differentiation, survival and cell proliferation. Collagen binding triggers a signaling pathway that involves SRC and leads to the activation of MAP kinases. Regulates remodeling of the extracellular matrix by up-regulation of the matrix metalloproteinases MMP2, MMP7 and MMP9, and thereby facilitates cell migration and wound healing. Required for normal blastocyst implantation during pregnancy, for normal mammary gland differentiation and normal lactation. Required for normal ear morphology and normal hearing (By similarity). Promotes smooth muscle cell migration, and thereby contributes to arterial wound healing. Also plays a role in tumor cell invasion. Phosphorylates PTPN11. {ECO:0000250, ECO:0000269\|PubMed:12065315, ECO:0000269\|PubMed:16234985, ECO:0000269\|PubMed:16337946, ECO:0000269\|PubMed:19401332, ECO:0000269\|PubMed:20093046, ECO:0000269\|PubMed:20432435, ECO:0000269\|PubMed:20884741, ECO:0000269\|PubMed:21044884, ECO:0000269\|PubMed:9659899}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000446312, ENST00000324771, ENST00000361741, ENST00000376567, ENST00000376568, ENST00000376569, ENST00000376570, ENST00000376575, ENST00000418800, ENST00000452441, ENST00000454612, ENST00000508312, ENST00000513240, ENST00000259875, ENST00000383377, ENST00000400410, ENST00000400411, ENST00000400414, ENST00000400486, ENST00000400488, ENST00000400489, ENST00000400491, ENST00000400492, ENST00000412329, ENST00000415092, ENST00000419412, ENST00000421229, ENST00000422628, ENST00000427053, ENST00000429699, ENST00000430933, ENST00000434428, ENST00000449518, ENST00000453510, ENST00000454774, ENST00000462241, ENST00000468225, ENST00000483193, ENST00000487780, ENST00000488414, ENST00000490712, ENST00000508472, ENST00000548133, ENST00000548693, ENST00000548962, ENST00000549026, ENST00000550384, ENST00000550395, ENST00000550666, ENST00000552068, ENST00000552434, ENST00000552721, ENST00000553015,	ENST00000278568, ENST00000356341, ENST00000528203, ENST00000530617, ENST00000525542,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 6 X 4=144	22 X 17 X 10=3740
	# samples	6	26
	** MAII score	log2(6/144*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(26/3740*10)=-3.84645474174655 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: DDR1 [Title/Abstract] AND PAK1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: DDR1 [Title/Abstract] AND PAK1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	DDR1(30861200)-PAK1(77070062), # samples:3
Anticipated loss of major functional domain due to fusion event.	DDR1-PAK1 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. DDR1-PAK1 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. DDR1-PAK1 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. DDR1-PAK1 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
Hgene	DDR1	GO:0038063	collagen-activated tyrosine kinase receptor signaling pathway	9659899\|21044884
Hgene	DDR1	GO:0038083	peptidyl-tyrosine autophosphorylation	21044884
Hgene	DDR1	GO:0046777	protein autophosphorylation	9659899
Tgene	PAK1	GO:0006357	regulation of transcription by RNA polymerase II	12514133
Tgene	PAK1	GO:0006468	protein phosphorylation	17332740
Tgene	PAK1	GO:0035407	histone H3-T11 phosphorylation	18066052

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:30861200/chr11:77070062)
- 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 DDR1 (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 PAK1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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)
ENST00000324771	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4623	1895	548	3055	835
ENST00000324771	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	4107	1895	548	2986	812
ENST00000324771	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3431	1895	548	3079	843
ENST00000324771	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3355	1895	548	3079	843
ENST00000418800	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4488	1760	353	2920	855
ENST00000418800	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3972	1760	353	2851	832
ENST00000418800	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3296	1760	353	2944	863
ENST00000418800	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3220	1760	353	2944	863
ENST00000454612	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4526	1798	451	2958	835
ENST00000454612	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	4010	1798	451	2889	812
ENST00000454612	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3334	1798	451	2982	843
ENST00000454612	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3258	1798	451	2982	843
ENST00000376569	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4367	1639	292	2799	835
ENST00000376569	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3851	1639	292	2730	812
ENST00000376569	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3175	1639	292	2823	843
ENST00000376569	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3099	1639	292	2823	843
ENST00000376575	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4408	1680	333	2840	835
ENST00000376575	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3892	1680	333	2771	812
ENST00000376575	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3216	1680	333	2864	843
ENST00000376575	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3140	1680	333	2864	843
ENST00000376570	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4408	1680	333	2840	835
ENST00000376570	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3892	1680	333	2771	812
ENST00000376570	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3216	1680	333	2864	843
ENST00000376570	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3140	1680	333	2864	843
ENST00000376568	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4370	1642	295	2802	835
ENST00000376568	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3854	1642	295	2733	812
ENST00000376568	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3178	1642	295	2826	843
ENST00000376568	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3102	1642	295	2826	843
ENST00000452441	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4334	1606	259	2766	835
ENST00000452441	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3818	1606	259	2697	812
ENST00000452441	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3142	1606	259	2790	843
ENST00000452441	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3066	1606	259	2790	843
ENST00000508312	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4381	1653	252	2813	853
ENST00000508312	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3865	1653	252	2744	830
ENST00000508312	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3189	1653	252	2837	861
ENST00000508312	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3113	1653	252	2837	861
ENST00000376567	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4416	1688	293	2848	851
ENST00000376567	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3900	1688	293	2779	828
ENST00000376567	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	3224	1688	293	2872	859
ENST00000376567	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	3148	1688	293	2872	859
ENST00000513240	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	4075	1347	0	2507	835
ENST00000513240	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	3559	1347	0	2438	812
ENST00000513240	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	2883	1347	0	2531	843
ENST00000513240	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	2807	1347	0	2531	843
ENST00000361741	DDR1	chr6	30861200	+	ENST00000356341	PAK1	chr11	77070062	-	3463	735	54	1895	613
ENST00000361741	DDR1	chr6	30861200	+	ENST00000530617	PAK1	chr11	77070062	-	2947	735	54	1826	590
ENST00000361741	DDR1	chr6	30861200	+	ENST00000278568	PAK1	chr11	77070062	-	2271	735	54	1919	621
ENST00000361741	DDR1	chr6	30861200	+	ENST00000528203	PAK1	chr11	77070062	-	2195	735	54	1919	621

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
ENST00000324771	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.00354635	0.99645364
ENST00000324771	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004507507	0.99549246
ENST00000324771	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005860102	0.9941399
ENST00000324771	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.007287622	0.9927124
ENST00000418800	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.002930601	0.9970694
ENST00000418800	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003844881	0.9961551
ENST00000418800	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004749602	0.99525034
ENST00000418800	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005931235	0.99406874
ENST00000454612	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003171575	0.9968284
ENST00000454612	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004040426	0.9959596
ENST00000454612	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005101979	0.994898
ENST00000454612	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.006366759	0.9936333
ENST00000376569	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003238619	0.9967614
ENST00000376569	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.00417776	0.9958222
ENST00000376569	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005536543	0.9944635
ENST00000376569	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.007001235	0.9929987
ENST00000376575	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003364295	0.99663574
ENST00000376575	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004303785	0.9956962
ENST00000376575	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005665423	0.9943346
ENST00000376575	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.007145989	0.99285406
ENST00000376570	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003364295	0.99663574
ENST00000376570	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004303785	0.9956962
ENST00000376570	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005665423	0.9943346
ENST00000376570	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.007145989	0.99285406
ENST00000376568	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003319103	0.9966809
ENST00000376568	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004245135	0.99575484
ENST00000376568	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005660356	0.99433964
ENST00000376568	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.007159812	0.9928402
ENST00000452441	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003379146	0.9966209
ENST00000452441	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004342227	0.9956578
ENST00000452441	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005765558	0.9942345
ENST00000452441	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.007286518	0.9927135
ENST00000508312	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003368288	0.9966317
ENST00000508312	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004332284	0.9956677
ENST00000508312	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005699435	0.9943006
ENST00000508312	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.007169371	0.9928307
ENST00000376567	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.002035717	0.99796426
ENST00000376567	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.002628157	0.9973718
ENST00000376567	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.003325224	0.9966748
ENST00000376567	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.004157855	0.99584216
ENST00000513240	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.002895839	0.9971041
ENST00000513240	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.00379967	0.99620026
ENST00000513240	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.005199905	0.9948001
ENST00000513240	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.006705619	0.9932943
ENST00000361741	ENST00000356341	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.00425238	0.9957476
ENST00000361741	ENST00000530617	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.00506943	0.99493057
ENST00000361741	ENST00000278568	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.009053835	0.9909462
ENST00000361741	ENST00000528203	DDR1	chr6	30861200	+	PAK1	chr11	77070062	-	0.011564052	0.988436

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

Top

Fusion Protein Breakpoint Sequences for DDR1-PAK1

+/-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
DDR1	chr6	30861200	PAK1	chr11	77070062	1347	449	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1606	449	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1639	449	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1642	449	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1653	467	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1680	449	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1688	465	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1760	469	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1798	449	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	1895	449	MLWRLHWRRLLSKNVKAVSETPAVPP
DDR1	chr6	30861200	PAK1	chr11	77070062	735	227	MLWRLHWRRLLSKNVKAVSETPAVPP

Top

Potential FusionNeoAntigen Information of DDR1-PAK1 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.

DDR1-PAK1_30861200_77070062.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)
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-B27:05	RRLLSKNVK	0.999	0.8653	7	16
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-A02:13	LLSKNVKAV	0.9914	0.5348	9	18
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-A02:11	RLLSKNVKA	0.9816	0.5452	8	17
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-A02:13	RLLSKNVKA	0.9508	0.5775	8	17
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-A02:29	RLLSKNVKA	0.844	0.5038	8	17
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-A02:20	RLLSKNVKA	0.8028	0.5049	8	17
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-A02:13	RLLSKNVKAV	0.9883	0.6092	8	18
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-A02:27	RLLSKNVKAV	0.9822	0.5233	8	18
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-B27:14	RRLLSKNVK	0.9986	0.7798	7	16
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-B27:03	RRLLSKNVK	0.9572	0.8882	7	16
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-B27:14	RRLLSKNVKA	0.9998	0.8201	7	17
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-B27:10	RRLLSKNVK	0.9985	0.7799	7	16
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-A02:03	LLSKNVKAV	0.998	0.5875	9	18
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	HLA-B27:08	RRLLSKNVK	0.9979	0.7189	7	16

Top

Potential FusionNeoAntigen Information of DDR1-PAK1 in HLA II

DDR1-PAK1_30861200_77070062.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)
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-0103	RLHWRRLLSKNVKAV	3	18
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-0103	WRLHWRRLLSKNVKA	2	17
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-0109	RLHWRRLLSKNVKAV	3	18
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-0115	RLHWRRLLSKNVKAV	3	18
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-0115	WRLHWRRLLSKNVKA	2	17
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-0906	SKNVKAVSETPAVPP	11	26
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-1503	SKNVKAVSETPAVPP	11	26
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-1503	LSKNVKAVSETPAVP	10	25
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-1523	SKNVKAVSETPAVPP	11	26
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-1523	LSKNVKAVSETPAVP	10	25
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-1609	RLHWRRLLSKNVKAV	3	18
DDR1-PAK1	chr6	30861200	chr11	77070062	1895	DRB1-1609	WRLHWRRLLSKNVKA	2	17

Top

Fusion breakpoint peptide structures of DDR1-PAK1

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
10538	WRRLLSKNVKAVSE	DDR1	PAK1	chr6	30861200	chr11	77070062	1895

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of DDR1-PAK1

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	10538	WRRLLSKNVKAVSE	-7.02924	-7.14264
HLA-B14:02	3BVN	10538	WRRLLSKNVKAVSE	-3.38077	-4.41607
HLA-B52:01	3W39	10538	WRRLLSKNVKAVSE	-6.41355	-6.52695
HLA-B52:01	3W39	10538	WRRLLSKNVKAVSE	-4.44188	-5.47718
HLA-A24:02	5HGA	10538	WRRLLSKNVKAVSE	-7.76595	-8.80125
HLA-A24:02	5HGA	10538	WRRLLSKNVKAVSE	-7.30892	-7.42232
HLA-B44:05	3DX8	10538	WRRLLSKNVKAVSE	-5.65486	-5.76826
HLA-B44:05	3DX8	10538	WRRLLSKNVKAVSE	-2.95775	-3.99305

Top

Vaccine Design for the FusionNeoAntigens of DDR1-PAK1

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
DDR1-PAK1	chr6	30861200	chr11	77070062	7	16	RRLLSKNVK	CGCAGGCTCCTCAGCAAGAATGTGAAG
DDR1-PAK1	chr6	30861200	chr11	77070062	7	17	RRLLSKNVKA	CGCAGGCTCCTCAGCAAGAATGTGAAGGCT
DDR1-PAK1	chr6	30861200	chr11	77070062	8	17	RLLSKNVKA	AGGCTCCTCAGCAAGAATGTGAAGGCT
DDR1-PAK1	chr6	30861200	chr11	77070062	8	18	RLLSKNVKAV	AGGCTCCTCAGCAAGAATGTGAAGGCTGTG
DDR1-PAK1	chr6	30861200	chr11	77070062	9	18	LLSKNVKAV	CTCCTCAGCAAGAATGTGAAGGCTGTG

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
DDR1-PAK1	chr6	30861200	chr11	77070062	10	25	LSKNVKAVSETPAVP	CTCAGCAAGAATGTGAAGGCTGTGTCTGAGACTCCTGCAGTGCCA
DDR1-PAK1	chr6	30861200	chr11	77070062	11	26	SKNVKAVSETPAVPP	AGCAAGAATGTGAAGGCTGTGTCTGAGACTCCTGCAGTGCCACCA
DDR1-PAK1	chr6	30861200	chr11	77070062	2	17	WRLHWRRLLSKNVKA	TGGCGGCTGCACTGGCGCAGGCTCCTCAGCAAGAATGTGAAGGCT
DDR1-PAK1	chr6	30861200	chr11	77070062	3	18	RLHWRRLLSKNVKAV	CGGCTGCACTGGCGCAGGCTCCTCAGCAAGAATGTGAAGGCTGTG

Top

Information of the samples that have these potential fusion neoantigens of DDR1-PAK1

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
OV	DDR1-PAK1	chr6	30861200	ENST00000324771	chr11	77070062	ENST00000278568	TCGA-13-1477-01A

Top

Potential target of CAR-T therapy development for DDR1-PAK1

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

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000324771

418_438

449

914.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000376567

418_438

449

877.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000376568

418_438

449

914.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000376569

418_438

449

877.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000376570

418_438

449

877.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000376575

418_438

449

920.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000418800

418_438

449

877.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000452441

418_438

449

914.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000454612

418_438

449

877.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000508312

418_438

467

895.0

Transmembrane

Helical

Hgene

DDR1

chr6:30861200

chr11:77070062

ENST00000513240

418_438

449

920.0

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

Top

Related Drugs to DDR1-PAK1

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to DDR1-PAK1

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)