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Fusion Protein:ILK-LPPR1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ILK-LPPR1
	FusionPDB ID: 39641
	FusionGDB2.0 ID: 39643
		Hgene	Tgene
	Gene symbol	ILK	LPPR1
	Gene ID	3611	54886
	Gene name	integrin linked kinase	phospholipid phosphatase related 1
	Synonyms	HEL-S-28\|ILK-1\|ILK-2\|P59\|p59ILK	LPPR1\|PRG-3
	Cytomap	11p15.4	9q31.1
	Type of gene	protein-coding	protein-coding
	Description	integrin-linked protein kinase59 kDa serine/threonine-protein kinaseepididymis secretory protein Li 28integrin-linked kinase-2	phospholipid phosphatase-related protein type 1lipid phosphate phosphatase-related protein type 1plasticity related gene 3plasticity-related gene 3 protein
	Modification date	20200320	20200313
	UniProtAcc	Q9H0C8 Main function of 5'-partner protein: FUNCTION: Protein phosphatase that may play a role in regulation of cell cycle progression via dephosphorylation of its substrates whose appropriate phosphorylation states might be crucial for cell proliferation. Selectively associates with integrin linked kinase (ILK), to modulate cell adhesion and growth factor signaling. Inhibits the ILK-GSK3B signaling axis and may play an important role in inhibiting oncogenic transformation. {ECO:0000269\|PubMed:14990992}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000299421, ENST00000396751, ENST00000420936, ENST00000528995, ENST00000526711, ENST00000537806,	ENST00000494890, ENST00000374874, ENST00000395056,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	4 X 6 X 2=48	2 X 4 X 2=16
	# samples	7	4
	** MAII score	log2(7/48*10)=0.54432051622381 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(4/16*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: ILK [Title/Abstract] AND LPPR1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ILK [Title/Abstract] AND LPPR1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ILK(6629441)-LPPR1(104075079), # samples:1 ILK(6629441)-LPPR1(104075080), # samples:1
Anticipated loss of major functional domain due to fusion event.	ILK-LPPR1 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. ILK-LPPR1 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	ILK	GO:0006468	protein phosphorylation	10871859
Hgene	ILK	GO:0007229	integrin-mediated signaling pathway	9366252

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:6629441/chr9:104075079)
- 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 ILK (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 LPPR1 (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)
ENST00000299421	ILK	chr11	6629441	+	ENST00000374874	LPPR1	chr9	104075079	+	1859	439	184	780	198
ENST00000299421	ILK	chr11	6629441	+	ENST00000395056	LPPR1	chr9	104075079	+	1855	439	184	780	198
ENST00000420936	ILK	chr11	6629441	+	ENST00000374874	LPPR1	chr9	104075079	+	1786	366	48	707	219
ENST00000420936	ILK	chr11	6629441	+	ENST00000395056	LPPR1	chr9	104075079	+	1782	366	48	707	219
ENST00000528995	ILK	chr11	6629441	+	ENST00000374874	LPPR1	chr9	104075079	+	1803	383	128	724	198
ENST00000528995	ILK	chr11	6629441	+	ENST00000395056	LPPR1	chr9	104075079	+	1799	383	128	724	198
ENST00000396751	ILK	chr11	6629441	+	ENST00000374874	LPPR1	chr9	104075079	+	2131	711	219	1052	277
ENST00000396751	ILK	chr11	6629441	+	ENST00000395056	LPPR1	chr9	104075079	+	2127	711	219	1052	277
ENST00000299421	ILK	chr11	6629441	+	ENST00000374874	LPPR1	chr9	104075080	+	1859	439	184	780	198
ENST00000299421	ILK	chr11	6629441	+	ENST00000395056	LPPR1	chr9	104075080	+	1855	439	184	780	198
ENST00000420936	ILK	chr11	6629441	+	ENST00000374874	LPPR1	chr9	104075080	+	1786	366	48	707	219
ENST00000420936	ILK	chr11	6629441	+	ENST00000395056	LPPR1	chr9	104075080	+	1782	366	48	707	219
ENST00000528995	ILK	chr11	6629441	+	ENST00000374874	LPPR1	chr9	104075080	+	1803	383	128	724	198
ENST00000528995	ILK	chr11	6629441	+	ENST00000395056	LPPR1	chr9	104075080	+	1799	383	128	724	198
ENST00000396751	ILK	chr11	6629441	+	ENST00000374874	LPPR1	chr9	104075080	+	2131	711	219	1052	277
ENST00000396751	ILK	chr11	6629441	+	ENST00000395056	LPPR1	chr9	104075080	+	2127	711	219	1052	277

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
ENST00000299421	ENST00000374874	ILK	chr11	6629441	+	LPPR1	chr9	104075079	+	0.002297975	0.99770206
ENST00000299421	ENST00000395056	ILK	chr11	6629441	+	LPPR1	chr9	104075079	+	0.002335445	0.9976646
ENST00000420936	ENST00000374874	ILK	chr11	6629441	+	LPPR1	chr9	104075079	+	0.003186808	0.99681324
ENST00000420936	ENST00000395056	ILK	chr11	6629441	+	LPPR1	chr9	104075079	+	0.003219204	0.99678075
ENST00000528995	ENST00000374874	ILK	chr11	6629441	+	LPPR1	chr9	104075079	+	0.004062502	0.99593747
ENST00000528995	ENST00000395056	ILK	chr11	6629441	+	LPPR1	chr9	104075079	+	0.004110504	0.9958895
ENST00000396751	ENST00000374874	ILK	chr11	6629441	+	LPPR1	chr9	104075079	+	0.006987919	0.99301213
ENST00000396751	ENST00000395056	ILK	chr11	6629441	+	LPPR1	chr9	104075079	+	0.00714633	0.9928537
ENST00000299421	ENST00000374874	ILK	chr11	6629441	+	LPPR1	chr9	104075080	+	0.002297975	0.99770206
ENST00000299421	ENST00000395056	ILK	chr11	6629441	+	LPPR1	chr9	104075080	+	0.002335445	0.9976646
ENST00000420936	ENST00000374874	ILK	chr11	6629441	+	LPPR1	chr9	104075080	+	0.003186808	0.99681324
ENST00000420936	ENST00000395056	ILK	chr11	6629441	+	LPPR1	chr9	104075080	+	0.003219204	0.99678075
ENST00000528995	ENST00000374874	ILK	chr11	6629441	+	LPPR1	chr9	104075080	+	0.004062502	0.99593747
ENST00000528995	ENST00000395056	ILK	chr11	6629441	+	LPPR1	chr9	104075080	+	0.004110504	0.9958895
ENST00000396751	ENST00000374874	ILK	chr11	6629441	+	LPPR1	chr9	104075080	+	0.006987919	0.99301213
ENST00000396751	ENST00000395056	ILK	chr11	6629441	+	LPPR1	chr9	104075080	+	0.00714633	0.9928537

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 ILK-LPPR1

+/-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
ILK	chr11	6629441	LPPR1	chr9	104075079	366	106	LAASHGHRDIVQKMYITSTIKTKSSR
ILK	chr11	6629441	LPPR1	chr9	104075079	383	85	LAASHGHRDIVQKMYITSTIKTKSSR
ILK	chr11	6629441	LPPR1	chr9	104075079	439	85	LAASHGHRDIVQKMYITSTIKTKSSR
ILK	chr11	6629441	LPPR1	chr9	104075079	711	164	LAASHGHRDIVQKMYITSTIKTKSSR
ILK	chr11	6629441	LPPR1	chr9	104075080	366	106	LAASHGHRDIVQKMYITSTIKTKSSR
ILK	chr11	6629441	LPPR1	chr9	104075080	383	85	LAASHGHRDIVQKMYITSTIKTKSSR
ILK	chr11	6629441	LPPR1	chr9	104075080	439	85	LAASHGHRDIVQKMYITSTIKTKSSR
ILK	chr11	6629441	LPPR1	chr9	104075080	711	164	LAASHGHRDIVQKMYITSTIKTKSSR

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Potential FusionNeoAntigen Information of ILK-LPPR1 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.

ILK-LPPR1_6629441_104075079.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)
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:01	HRDIVQKM	0.9992	0.8012	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B38:02	HRDIVQKM	0.9983	0.8878	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:10	HRDIVQKM	0.9934	0.5516	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:18	HRDIVQKM	0.9785	0.734	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:37	HRDIVQKM	0.9722	0.6112	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B52:01	KMYITSTI	0.8204	0.6638	12	20
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-A30:08	KMYITSTIK	0.995	0.6363	12	21
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:01	GHRDIVQKM	0.9829	0.7898	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:06	GHRDIVQKM	0.9725	0.7312	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B27:04	HRDIVQKMY	0.9565	0.7633	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B27:05	HRDIVQKMY	0.93	0.8926	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B27:02	HRDIVQKMY	0.929	0.705	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B14:01	GHRDIVQKM	0.9164	0.6555	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B14:02	GHRDIVQKM	0.9164	0.6555	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B38:01	GHRDIVQKM	0.9152	0.8559	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B38:02	GHRDIVQKM	0.9082	0.846	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:18	GHRDIVQKM	0.5573	0.6726	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:37	GHRDIVQKM	0.4552	0.5335	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:03	HRDIVQKMY	0.4516	0.8197	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:03	GHRDIVQKM	0.4471	0.7126	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:18	HRDIVQKMY	0.445	0.755	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B48:01	GHRDIVQKM	0.2308	0.5091	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B52:01	QKMYITSTI	0.1816	0.8021	11	20
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:18	HGHRDIVQKM	0.9388	0.6743	4	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:18	GHRDIVQKMY	0.8722	0.7126	5	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:10	HGHRDIVQKM	0.7285	0.503	4	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:37	HGHRDIVQKM	0.5824	0.5128	4	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B07:10	HGHRDIVQKM	0.512	0.5271	4	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B38:01	SHGHRDIVQKM	0.9929	0.8697	3	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B38:02	SHGHRDIVQKM	0.992	0.8625	3	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-A30:08	KMYITSTIKTK	0.9901	0.6794	12	23
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:95	HRDIVQKM	0.9994	0.7456	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:09	HRDIVQKM	0.9993	0.5317	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:05	HRDIVQKM	0.9992	0.9668	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:13	HRDIVQKM	0.999	0.8902	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:27	HRDIVQKM	0.999	0.967	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:12	HRDIVQKM	0.9988	0.8042	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:29	HRDIVQKM	0.998	0.9199	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:19	HRDIVQKM	0.9978	0.7658	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:05	HRDIVQKM	0.9975	0.7996	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:80	HRDIVQKM	0.9974	0.9609	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:67	HRDIVQKM	0.9974	0.9609	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:46	HRDIVQKM	0.9972	0.9032	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:10	HRDIVQKM	0.9972	0.9617	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C12:16	HRDIVQKM	0.9473	0.9686	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:09	GHRDIVQKM	0.9878	0.5023	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:95	HRDIVQKMY	0.9822	0.7424	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:12	GHRDIVQKM	0.9792	0.7975	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:05	HRDIVQKMY	0.9728	0.9643	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:27	HRDIVQKMY	0.9602	0.9626	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:05	GHRDIVQKM	0.9138	0.7729	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B27:14	HRDIVQKMY	0.8691	0.8393	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:04	VQKMYITST	0.8448	0.7044	10	19
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:19	HRDIVQKMY	0.8298	0.76	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:80	HRDIVQKMY	0.7935	0.956	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:67	HRDIVQKMY	0.7935	0.956	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:10	HRDIVQKMY	0.7859	0.9603	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:46	HRDIVQKMY	0.7571	0.9074	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:95	GHRDIVQKM	0.7231	0.5672	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B27:03	HRDIVQKMY	0.6487	0.9007	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:27	GHRDIVQKM	0.6209	0.9369	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:05	GHRDIVQKM	0.6033	0.9467	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:29	GHRDIVQKM	0.5475	0.8742	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:67	GHRDIVQKM	0.5463	0.9458	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:80	GHRDIVQKM	0.5463	0.9458	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:10	GHRDIVQKM	0.5435	0.9474	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:19	GHRDIVQKM	0.5383	0.624	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:46	GHRDIVQKM	0.5356	0.8602	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:13	GHRDIVQKM	0.5322	0.8951	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B14:03	GHRDIVQKM	0.2507	0.7393	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C12:16	GHRDIVQKM	0.1317	0.9592	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C12:16	HRDIVQKMY	0.0393	0.9646	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C18:01	HRDIVQKM	0.9998	0.8011	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:01	HRDIVQKM	0.9995	0.7428	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:31	HRDIVQKM	0.9993	0.8008	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:22	HRDIVQKM	0.9976	0.6813	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:02	HRDIVQKM	0.9974	0.9609	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:06	HRDIVQKM	0.9969	0.9909	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:17	HRDIVQKM	0.9952	0.9686	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:08	HRDIVQKM	0.9743	0.9934	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:09	HRDIVQKM	0.9679	0.6113	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:17	HRDIVQKM	0.9075	0.9946	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:02	HRDIVQKM	0.9075	0.9946	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:11	HRDIVQKM	0.8864	0.589	6	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-A30:01	KMYITSTIK	0.9946	0.7717	12	21
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:02	GHRDIVQKM	0.9818	0.8139	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:01	HRDIVQKMY	0.9815	0.7383	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:31	GHRDIVQKM	0.9655	0.7905	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B27:10	HRDIVQKMY	0.9469	0.8665	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B27:08	HRDIVQKMY	0.9246	0.7876	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B38:05	GHRDIVQKM	0.9152	0.8559	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:17	HRDIVQKMY	0.7972	0.9628	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:02	HRDIVQKMY	0.7935	0.956	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:22	HRDIVQKMY	0.7305	0.6898	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:01	GHRDIVQKM	0.6301	0.5452	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:17	GHRDIVQKM	0.5751	0.9631	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:02	GHRDIVQKM	0.5463	0.9458	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C07:22	GHRDIVQKM	0.5257	0.5925	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B39:11	GHRDIVQKM	0.5252	0.6249	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:09	GHRDIVQKM	0.4366	0.6115	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:08	HRDIVQKMY	0.3227	0.9917	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:06	HRDIVQKMY	0.2876	0.9909	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:06	GHRDIVQKM	0.2107	0.9887	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:08	GHRDIVQKM	0.1745	0.9929	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:68	GHRDIVQKM	0.1357	0.5078	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:54	GHRDIVQKM	0.1196	0.8023	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:02	GHRDIVQKM	0.1152	0.9933	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:17	GHRDIVQKM	0.1152	0.9933	5	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:68	HRDIVQKMY	0.0224	0.6843	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:02	HRDIVQKMY	0.0133	0.9934	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-C06:17	HRDIVQKMY	0.0133	0.9934	6	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:54	GHRDIVQKMY	0.8672	0.8578	5	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:68	GHRDIVQKMY	0.849	0.5499	5	15
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B15:09	HGHRDIVQKM	0.226	0.6743	4	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-B38:05	SHGHRDIVQKM	0.9929	0.8697	3	14
ILK-LPPR1	chr11	6629441	chr9	104075079	439	HLA-A30:01	KMYITSTIKTK	0.9904	0.8027	12	23

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Potential FusionNeoAntigen Information of ILK-LPPR1 in HLA II

ILK-LPPR1_6629441_104075079.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)
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-0820	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-0831	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-1106	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-1147	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-1150	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-1154	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-1156	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-1183	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-1188	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB1-1418	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB5-0112	QKMYITSTIKTKSSR	11	26
ILK-LPPR1	chr11	6629441	chr9	104075079	439	DRB5-0112	VQKMYITSTIKTKSS	10	25

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Fusion breakpoint peptide structures of ILK-LPPR1

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
3479	HRDIVQKMYITSTI	ILK	LPPR1	chr11	6629441	chr9	104075079	439

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ILK-LPPR1

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	3479	HRDIVQKMYITSTI	-7.15543	-7.26883
HLA-B14:02	3BVN	3479	HRDIVQKMYITSTI	-4.77435	-5.80965
HLA-B52:01	3W39	3479	HRDIVQKMYITSTI	-6.80875	-6.92215
HLA-B52:01	3W39	3479	HRDIVQKMYITSTI	-4.20386	-5.23916
HLA-A11:01	4UQ2	3479	HRDIVQKMYITSTI	-7.5194	-8.5547
HLA-A11:01	4UQ2	3479	HRDIVQKMYITSTI	-6.9601	-7.0735
HLA-A24:02	5HGA	3479	HRDIVQKMYITSTI	-7.52403	-7.63743
HLA-A24:02	5HGA	3479	HRDIVQKMYITSTI	-5.82433	-6.85963
HLA-B27:05	6PYJ	3479	HRDIVQKMYITSTI	-3.28285	-4.31815
HLA-B44:05	3DX8	3479	HRDIVQKMYITSTI	-5.91172	-6.94702
HLA-B44:05	3DX8	3479	HRDIVQKMYITSTI	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of ILK-LPPR1

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
ILK-LPPR1	chr11	6629441	chr9	104075079	10	19	VQKMYITST	GTACAGAAGATGTATATTACAAGCACA
ILK-LPPR1	chr11	6629441	chr9	104075079	11	20	QKMYITSTI	CAGAAGATGTATATTACAAGCACAATC
ILK-LPPR1	chr11	6629441	chr9	104075079	12	20	KMYITSTI	AAGATGTATATTACAAGCACAATC
ILK-LPPR1	chr11	6629441	chr9	104075079	12	21	KMYITSTIK	AAGATGTATATTACAAGCACAATCAAG
ILK-LPPR1	chr11	6629441	chr9	104075079	12	23	KMYITSTIKTK	AAGATGTATATTACAAGCACAATCAAGACGAAG
ILK-LPPR1	chr11	6629441	chr9	104075079	3	14	SHGHRDIVQKM	AGTCATGGACACCGTGATATTGTACAGAAGATG
ILK-LPPR1	chr11	6629441	chr9	104075079	4	14	HGHRDIVQKM	CATGGACACCGTGATATTGTACAGAAGATG
ILK-LPPR1	chr11	6629441	chr9	104075079	5	14	GHRDIVQKM	GGACACCGTGATATTGTACAGAAGATG
ILK-LPPR1	chr11	6629441	chr9	104075079	5	15	GHRDIVQKMY	GGACACCGTGATATTGTACAGAAGATGTAT
ILK-LPPR1	chr11	6629441	chr9	104075079	6	14	HRDIVQKM	CACCGTGATATTGTACAGAAGATG
ILK-LPPR1	chr11	6629441	chr9	104075079	6	15	HRDIVQKMY	CACCGTGATATTGTACAGAAGATGTAT

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
ILK-LPPR1	chr11	6629441	chr9	104075079	10	25	VQKMYITSTIKTKSS	GTACAGAAGATGTATATTACAAGCACAATCAAGACGAAGAGCAGT
ILK-LPPR1	chr11	6629441	chr9	104075079	11	26	QKMYITSTIKTKSSR	CAGAAGATGTATATTACAAGCACAATCAAGACGAAGAGCAGTCGA

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Information of the samples that have these potential fusion neoantigens of ILK-LPPR1

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	ILK-LPPR1	chr11	6629441	ENST00000299421	chr9	104075079	ENST00000374874	TCGA-24-1434

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Potential target of CAR-T therapy development for ILK-LPPR1

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

LPPR1

chr11:6629441

chr9:104075079

ENST00000374874

230_247

326.0

Transmembrane

Helical

Tgene

LPPR1

chr11:6629441

chr9:104075079

ENST00000374874

257_277

326.0

Transmembrane

Helical

Tgene

LPPR1

chr11:6629441

chr9:104075079

ENST00000395056

230_247

326.0

Transmembrane

Helical

Tgene

LPPR1

chr11:6629441

chr9:104075079

ENST00000395056

257_277

326.0

Transmembrane

Helical

Tgene

LPPR1

chr11:6629441

chr9:104075080

ENST00000374874

230_247

326.0

Transmembrane

Helical

Tgene

LPPR1

chr11:6629441

chr9:104075080

ENST00000374874

257_277

326.0

Transmembrane

Helical

Tgene

LPPR1

chr11:6629441

chr9:104075080

ENST00000395056

230_247

326.0

Transmembrane

Helical

Tgene

LPPR1

chr11:6629441

chr9:104075080

ENST00000395056

257_277

326.0

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 ILK-LPPR1

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 ILK-LPPR1

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)