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Fusion Protein:SMYD2-PROX1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SMYD2-PROX1
	FusionPDB ID: 84362
	FusionGDB2.0 ID: 84362
		Hgene	Tgene
	Gene symbol	SMYD2	PROX1
	Gene ID	56950	5629
	Gene name	SET and MYND domain containing 2	prospero homeobox 1
	Synonyms	HSKM-B\|KMT3C\|ZMYND14	-
	Cytomap	1q32.3	1q32.3
	Type of gene	protein-coding	protein-coding
	Description	N-lysine methyltransferase SMYD2SET and MYND domain-containing protein 2histone methyltransferase SMYD2lysine N-methyltransferase 3Czinc finger, MYND domain containing 14	prospero homeobox protein 1homeobox prospero-like protein PROX1prospero-related homeobox 1
	Modification date	20200320	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000491455, ENST00000366957, ENST00000415093,	ENST00000261454, ENST00000366958, ENST00000435016, ENST00000498508, ENST00000607726,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	10 X 7 X 7=490	4 X 4 X 3=48
	# samples	11	4
	** MAII score	log2(11/490*10)=-2.15527822547791 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SMYD2 [Title/Abstract] AND PROX1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SMYD2 [Title/Abstract] AND PROX1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SMYD2(214501067)-PROX1(214208992), # samples:3 PROX1(214178615)-SMYD2(214488105), # samples:1
Anticipated loss of major functional domain due to fusion event.	SMYD2-PROX1 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. SMYD2-PROX1 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. SMYD2-PROX1 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. SMYD2-PROX1 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. SMYD2-PROX1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. SMYD2-PROX1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. SMYD2-PROX1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF. SMYD2-PROX1 seems lost the major protein functional domain in Tgene 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	SMYD2	GO:0018026	peptidyl-lysine monomethylation	17108971\|20870719
Tgene	PROX1	GO:0000122	negative regulation of transcription by RNA polymerase II	15205472
Tgene	PROX1	GO:0001938	positive regulation of endothelial cell proliferation	19210544
Tgene	PROX1	GO:0001946	lymphangiogenesis	12412020
Tgene	PROX1	GO:0008284	positive regulation of cell proliferation	12198161
Tgene	PROX1	GO:0010468	regulation of gene expression	12198161
Tgene	PROX1	GO:0010595	positive regulation of endothelial cell migration	19210544
Tgene	PROX1	GO:0043433	negative regulation of DNA-binding transcription factor activity	15205472\|16488887
Tgene	PROX1	GO:0045071	negative regulation of viral genome replication	19264593
Tgene	PROX1	GO:0045737	positive regulation of cyclin-dependent protein serine/threonine kinase activity	19210544
Tgene	PROX1	GO:0045892	negative regulation of transcription, DNA-templated	15143342\|15205472
Tgene	PROX1	GO:0060836	lymphatic endothelial cell differentiation	12198161

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:214501067/chr1:214208992)
- 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 SMYD2 (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 PROX1 (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)

ENST00000415093

SMYD2

chr1

214501067

ENST00000366958

PROX1

chr1

214208992

6331

727

912

296

ENST00000366957

SMYD2

chr1

214501067

ENST00000366958

PROX1

chr1

214208992

6331

727

912

296

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
ENST00000415093	ENST00000366958	SMYD2	chr1	214501067	+	PROX1	chr1	214208992	+	0.000239127	0.9997609
ENST00000366957	ENST00000366958	SMYD2	chr1	214501067	+	PROX1	chr1	214208992	+	0.000239127	0.9997609

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 SMYD2-PROX1

+/-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
SMYD2	chr1	214501067	PROX1	chr1	214208992	727	235	EVRAVQEIKPGEEVPERFLEVAQITL

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Potential FusionNeoAntigen Information of SMYD2-PROX1 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.

SMYD2-PROX1_214501067_214208992.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)
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B18:01	EEVPERFL	0.9988	0.9789	11	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A66:01	EVPERFLEV	0.9997	0.6913	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:02	QEIKPGEEV	0.9989	0.8694	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A26:03	EVPERFLEV	0.9988	0.701	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B45:01	QEIKPGEEV	0.9988	0.9849	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:01	QEIKPGEEV	0.9921	0.7256	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A26:02	EVPERFLEV	0.9907	0.5907	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A26:14	EVPERFLEV	0.9724	0.709	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A26:15	EVPERFLEV	0.9724	0.709	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B08:09	EVPERFLEV	0.9714	0.5956	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B41:01	QEIKPGEEV	0.9312	0.9888	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:05	QEIKPGEEV	0.9113	0.7248	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:02	QEIKPGEEV	0.8967	0.6098	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:03	QEIKPGEEV	0.8949	0.9819	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B47:01	QEIKPGEEV	0.8562	0.7866	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A02:21	EVPERFLEV	0.8552	0.5667	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:05	QEIKPGEEV	0.8045	0.5953	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B47:01	GEEVPERFL	0.7883	0.6771	10	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B41:02	QEIKPGEEV	0.7592	0.5808	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:01	QEIKPGEEV	0.7329	0.9822	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B39:13	QEIKPGEEV	0.5762	0.9917	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B41:01	GEEVPERFL	0.315	0.9675	10	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B39:13	GEEVPERFL	0.1254	0.9864	10	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B45:01	QEIKPGEEVP	0.9879	0.9781	5	15
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:02	QEIKPGEEVP	0.9867	0.8745	5	15
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:01	QEIKPGEEVP	0.9315	0.9829	5	15
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B41:01	QEIKPGEEVP	0.931	0.9842	5	15
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B53:01	KPGEEVPERF	0.759	0.6925	8	18
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B45:01	EEVPERFLEVA	0.9992	0.8823	11	22
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:02	EEVPERFLEVA	0.9974	0.7299	11	22
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:01	AVQEIKPGEEV	0.9344	0.7857	3	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:06	QEIKPGEEV	0.9996	0.7992	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-C04:06	EVPERFLEV	0.9842	0.9408	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:10	QEIKPGEEV	0.976	0.8186	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A26:01	EVPERFLEV	0.9724	0.709	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B48:03	QEIKPGEEV	0.9704	0.7768	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:09	QEIKPGEEV	0.9427	0.7247	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-C04:14	EVPERFLEV	0.9403	0.7882	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:03	QEIKPGEEV	0.9192	0.6425	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:08	QEIKPGEEV	0.918	0.6802	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B78:01	EVPERFLEV	0.8785	0.521	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-C01:17	EVPERFLEV	0.8285	0.9368	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-C01:30	EVPERFLEV	0.6766	0.9592	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B39:08	QEIKPGEEV	0.6736	0.9804	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B39:08	GEEVPERFL	0.4199	0.9174	10	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-C07:29	EVPERFLEV	0.3061	0.9415	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:10	EEVPERFLEV	0.9621	0.5001	11	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B18:05	EEVPERFL	0.9988	0.9789	11	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B18:03	EEVPERFL	0.9978	0.9774	11	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A69:01	EVPERFLEV	0.9988	0.704	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:04	QEIKPGEEV	0.9979	0.9414	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:04	GEEVPERFL	0.994	0.7225	10	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A25:01	EVPERFLEV	0.9935	0.8582	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:36	QEIKPGEEV	0.9929	0.7462	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:49	QEIKPGEEV	0.9905	0.7414	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:12	QEIKPGEEV	0.9704	0.7768	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-C01:03	EVPERFLEV	0.9453	0.9356	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B41:03	QEIKPGEEV	0.9372	0.9266	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:22	QEIKPGEEV	0.8967	0.6098	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:13	QEIKPGEEV	0.8949	0.9819	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:07	QEIKPGEEV	0.8949	0.9819	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B44:26	QEIKPGEEV	0.8949	0.9819	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-C01:02	EVPERFLEV	0.8715	0.9361	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A02:06	EVPERFLEV	0.8552	0.5667	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B08:12	EVPERFLEV	0.8457	0.5352	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B18:11	QEIKPGEEV	0.7618	0.9333	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:04	QEIKPGEEV	0.7329	0.9822	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:05	QEIKPGEEV	0.7329	0.9822	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-C07:04	EVPERFLEV	0.6803	0.8917	12	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B39:11	QEIKPGEEV	0.6282	0.9637	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B41:03	GEEVPERFL	0.4274	0.7107	10	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B39:02	QEIKPGEEV	0.4112	0.9915	5	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B39:02	GEEVPERFL	0.1409	0.9865	10	19
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:04	QEIKPGEEVP	0.9315	0.9829	5	15
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B50:05	QEIKPGEEVP	0.9315	0.9829	5	15
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-A68:02	EEVPERFLEV	0.9304	0.513	11	21
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:04	AVQEIKPGEEV	0.9553	0.9599	3	14
SMYD2-PROX1	chr1	214501067	chr1	214208992	727	HLA-B40:36	AVQEIKPGEEV	0.9412	0.801	3	14

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Potential FusionNeoAntigen Information of SMYD2-PROX1 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 SMYD2-PROX1

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
1797	EIKPGEEVPERFLE	SMYD2	PROX1	chr1	214501067	chr1	214208992	727

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SMYD2-PROX1

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	1797	EIKPGEEVPERFLE	-7.9962	-8.1096
HLA-B14:02	3BVN	1797	EIKPGEEVPERFLE	-5.70842	-6.74372
HLA-B52:01	3W39	1797	EIKPGEEVPERFLE	-6.83737	-6.95077
HLA-B52:01	3W39	1797	EIKPGEEVPERFLE	-4.4836	-5.5189
HLA-A11:01	4UQ2	1797	EIKPGEEVPERFLE	-10.0067	-10.1201
HLA-A11:01	4UQ2	1797	EIKPGEEVPERFLE	-9.03915	-10.0745
HLA-A24:02	5HGA	1797	EIKPGEEVPERFLE	-6.56204	-6.67544
HLA-A24:02	5HGA	1797	EIKPGEEVPERFLE	-5.42271	-6.45801
HLA-B44:05	3DX8	1797	EIKPGEEVPERFLE	-7.85648	-8.89178
HLA-B44:05	3DX8	1797	EIKPGEEVPERFLE	-5.3978	-5.5112
HLA-A02:01	6TDR	1797	EIKPGEEVPERFLE	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of SMYD2-PROX1

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
SMYD2-PROX1	chr1	214501067	chr1	214208992	10	19	GEEVPERFL	GGAGAGGAGGTTCCAGAGAGATTCCTG
SMYD2-PROX1	chr1	214501067	chr1	214208992	11	19	EEVPERFL	GAGGAGGTTCCAGAGAGATTCCTG
SMYD2-PROX1	chr1	214501067	chr1	214208992	11	21	EEVPERFLEV	GAGGAGGTTCCAGAGAGATTCCTGGAAGTT
SMYD2-PROX1	chr1	214501067	chr1	214208992	11	22	EEVPERFLEVA	GAGGAGGTTCCAGAGAGATTCCTGGAAGTTGCT
SMYD2-PROX1	chr1	214501067	chr1	214208992	12	21	EVPERFLEV	GAGGTTCCAGAGAGATTCCTGGAAGTT
SMYD2-PROX1	chr1	214501067	chr1	214208992	3	14	AVQEIKPGEEV	GCTGTACAGGAAATCAAGCCGGGAGAGGAGGTT
SMYD2-PROX1	chr1	214501067	chr1	214208992	5	14	QEIKPGEEV	CAGGAAATCAAGCCGGGAGAGGAGGTT
SMYD2-PROX1	chr1	214501067	chr1	214208992	5	15	QEIKPGEEVP	CAGGAAATCAAGCCGGGAGAGGAGGTTCCA
SMYD2-PROX1	chr1	214501067	chr1	214208992	8	18	KPGEEVPERF	AAGCCGGGAGAGGAGGTTCCAGAGAGATTC

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 SMYD2-PROX1

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
LIHC	SMYD2-PROX1	chr1	214501067	ENST00000366957	chr1	214208992	ENST00000366958	TCGA-ED-A7PX-01A

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Potential target of CAR-T therapy development for SMYD2-PROX1

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 SMYD2-PROX1

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 SMYD2-PROX1

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)