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Fusion Protein:HYI-NFIA

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: HYI-NFIA
	FusionPDB ID: 38140
	FusionGDB2.0 ID: 38140
		Hgene	Tgene
	Gene symbol	HYI	NFIA
	Gene ID	81888	4774
	Gene name	hydroxypyruvate isomerase (putative)	nuclear factor I A
	Synonyms	HT036	BRMUTD\|CTF\|NF-I/A\|NF1-A\|NFI-A\|NFI-L
	Cytomap	1p34.2	1p31.3
	Type of gene	protein-coding	protein-coding
	Description	putative hydroxypyruvate isomeraseendothelial cell apoptosis protein E-CE1hydroxypyruvate isomerase homolog	nuclear factor 1 A-typeCCAAT-box-binding transcription factorTGGCA-binding protein
	Modification date	20200313	20200313
	UniProtAcc	Q5T013 Main function of 5'-partner protein: FUNCTION: Catalyzes the reversible isomerization between hydroxypyruvate and 2-hydroxy-3-oxopropanoate (also termed tartronate semialdehyde). {ECO:0000250}.	Q12857 Main function of 5'-partner protein: FUNCTION: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000372425, ENST00000372426, ENST00000372432, ENST00000372434, ENST00000486909, ENST00000583037,	ENST00000371185, ENST00000371187, ENST00000371189, ENST00000403491, ENST00000479364, ENST00000485903, ENST00000357977, ENST00000371184, ENST00000371191, ENST00000407417,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 6 X 3=54	21 X 24 X 8=4032
	# samples	6	28
	** MAII score	log2(6/54*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(28/4032*10)=-3.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: HYI [Title/Abstract] AND NFIA [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: HYI [Title/Abstract] AND NFIA [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	HYI(43917319)-NFIA(61798184), # samples:3
Anticipated loss of major functional domain due to fusion event.	HYI-NFIA 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. HYI-NFIA 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. HYI-NFIA 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. HYI-NFIA 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. HYI-NFIA seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. HYI-NFIA seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
Tgene	NFIA	GO:0045944	positive regulation of transcription by RNA polymerase II	17010934

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:43917319/chr1:61798184)
- 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 HYI (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 NFIA (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)
ENST00000372425	HYI	chr1	43917319	-	ENST00000371191	NFIA	chr1	61798184	+	1931	821	196	1725	509
ENST00000372425	HYI	chr1	43917319	-	ENST00000407417	NFIA	chr1	61798184	+	1991	821	196	1725	509
ENST00000372434	HYI	chr1	43917319	-	ENST00000371191	NFIA	chr1	61798184	+	1842	732	32	1636	534
ENST00000372434	HYI	chr1	43917319	-	ENST00000407417	NFIA	chr1	61798184	+	1902	732	32	1636	534
ENST00000372432	HYI	chr1	43917319	-	ENST00000371191	NFIA	chr1	61798184	+	1905	795	170	1699	509
ENST00000372432	HYI	chr1	43917319	-	ENST00000407417	NFIA	chr1	61798184	+	1965	795	170	1699	509
ENST00000372426	HYI	chr1	43917319	-	ENST00000371191	NFIA	chr1	61798184	+	1591	481	0	1385	461
ENST00000372426	HYI	chr1	43917319	-	ENST00000407417	NFIA	chr1	61798184	+	1651	481	0	1385	461
ENST00000486909	HYI	chr1	43917319	-	ENST00000371191	NFIA	chr1	61798184	+	1790	680	55	1584	509
ENST00000486909	HYI	chr1	43917319	-	ENST00000407417	NFIA	chr1	61798184	+	1850	680	55	1584	509

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
ENST00000372425	ENST00000371191	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.061803672	0.93819636
ENST00000372425	ENST00000407417	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.048782874	0.9512171
ENST00000372434	ENST00000371191	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.06436345	0.9356366
ENST00000372434	ENST00000407417	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.05018557	0.94981444
ENST00000372432	ENST00000371191	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.062494524	0.9375055
ENST00000372432	ENST00000407417	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.049324553	0.9506754
ENST00000372426	ENST00000371191	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.08954266	0.9104574
ENST00000372426	ENST00000407417	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.06961478	0.93038523
ENST00000486909	ENST00000371191	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.06503011	0.9349699
ENST00000486909	ENST00000407417	HYI	chr1	43917319	-	NFIA	chr1	61798184	+	0.050093062	0.9499069

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 HYI-NFIA

+/-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
HYI	chr1	43917319	NFIA	chr1	61798184	481	160	NLTGNIREFLPIVGHLGFQDSFVTSG
HYI	chr1	43917319	NFIA	chr1	61798184	680	208	NLTGNIREFLPIVGHLGFQDSFVTSG
HYI	chr1	43917319	NFIA	chr1	61798184	732	233	NLTGNIREFLPIVGHLGFQDSFVTSG
HYI	chr1	43917319	NFIA	chr1	61798184	795	208	NLTGNIREFLPIVGHLGFQDSFVTSG
HYI	chr1	43917319	NFIA	chr1	61798184	821	208	NLTGNIREFLPIVGHLGFQDSFVTSG

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Potential FusionNeoAntigen Information of HYI-NFIA 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.

HYI-NFIA_43917319_61798184.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)
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:01	LPIVGHLGF	0.9982	0.7596	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:08	LPIVGHLGF	0.9936	0.8043	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:03	LPIVGHLGF	0.9877	0.7696	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B15:02	LPIVGHLGF	0.9872	0.8279	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B47:01	REFLPIVGH	0.9417	0.6257	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B18:01	REFLPIVGH	0.8579	0.9469	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:04	LPIVGHLGF	0.8472	0.7686	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:02	LPIVGHLGF	0.8472	0.7686	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B50:02	REFLPIVGH	0.7949	0.5971	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B50:01	REFLPIVGH	0.0111	0.6138	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B13:01	REFLPIVGHL	0.9839	0.8286	6	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B47:01	REFLPIVGHL	0.9813	0.6012	6	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:05	FLPIVGHLGF	0.9433	0.5392	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:01	FLPIVGHLGF	0.9205	0.9123	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B39:13	REFLPIVGHL	0.8476	0.9764	6	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B38:01	VGHLGFQDSF	0.3715	0.976	12	22
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B38:02	VGHLGFQDSF	0.2967	0.9771	12	22
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-C01:17	FLPIVGHL	0.9943	0.9696	8	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-A02:07	FLPIVGHL	0.9903	0.6567	8	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-C01:30	FLPIVGHL	0.9621	0.9771	8	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B15:31	LPIVGHLGF	0.9981	0.7194	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B15:21	LPIVGHLGF	0.9868	0.8147	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:12	LPIVGHLGF	0.8472	0.7686	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B42:02	LPIVGHLGF	0.5518	0.848	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B39:10	LPIVGHLGF	0.534	0.7281	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B42:01	LPIVGHLGF	0.3975	0.8431	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B40:06	REFLPIVGHL	0.9986	0.5825	6	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B27:14	IREFLPIVGH	0.9982	0.8277	5	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-C01:02	FLPIVGHL	0.9948	0.9705	8	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-C01:03	FLPIVGHL	0.9841	0.9061	8	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:77	LPIVGHLGF	0.9982	0.7596	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:23	LPIVGHLGF	0.9981	0.789	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:20	LPIVGHLGF	0.9978	0.8035	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:30	LPIVGHLGF	0.9953	0.5877	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:17	LPIVGHLGF	0.9953	0.5877	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:24	LPIVGHLGF	0.9932	0.7911	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:11	LPIVGHLGF	0.9877	0.8077	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:13	LPIVGHLGF	0.9856	0.769	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B15:13	LPIVGHLGF	0.9423	0.5669	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B18:05	REFLPIVGH	0.8579	0.9469	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B78:02	LPIVGHLGF	0.8567	0.5284	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B18:08	REFLPIVGH	0.8565	0.8583	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:09	LPIVGHLGF	0.8472	0.7686	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B18:06	REFLPIVGH	0.8095	0.9545	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B18:04	LPIVGHLGF	0.7666	0.6789	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B18:11	REFLPIVGH	0.6394	0.9365	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B67:01	LPIVGHLGF	0.6296	0.6563	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B18:07	LPIVGHLGF	0.524	0.5835	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B15:08	LPIVGHLGF	0.1816	0.6635	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:43	LPIVGHLGF	0.1767	0.6794	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B15:11	LPIVGHLGF	0.1695	0.6315	9	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B15:53	REFLPIVGH	0.0204	0.955	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B50:05	REFLPIVGH	0.0111	0.6138	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B50:04	REFLPIVGH	0.0111	0.6138	6	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B15:08	FLPIVGHLGF	0.9986	0.7802	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:43	FLPIVGHLGF	0.9982	0.7947	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B27:10	IREFLPIVGH	0.9975	0.869	5	15
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B40:04	REFLPIVGHL	0.9949	0.6274	6	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:11	FLPIVGHLGF	0.9759	0.881	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:30	FLPIVGHLGF	0.9482	0.7123	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:17	FLPIVGHLGF	0.9482	0.7123	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:23	FLPIVGHLGF	0.9239	0.9232	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:77	FLPIVGHLGF	0.9205	0.9123	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B39:02	REFLPIVGHL	0.8949	0.9775	6	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B35:24	FLPIVGHLGF	0.8425	0.9066	8	18
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B41:03	REFLPIVGHL	0.6557	0.7533	6	16
HYI-NFIA	chr1	43917319	chr1	61798184	821	HLA-B38:05	VGHLGFQDSF	0.3715	0.976	12	22

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Potential FusionNeoAntigen Information of HYI-NFIA in HLA II

HYI-NFIA_43917319_61798184.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)
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0101	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0103	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0103	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0103	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0105	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0107	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0109	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0109	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0109	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0111	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0113	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0115	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0115	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0115	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0117	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0119	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0121	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0125	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0127	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0129	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0129	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0131	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0447	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0447	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-0454	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1130	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1130	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1216	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1367	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1446	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1515	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1527	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1601	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1601	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1601	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1602	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1603	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1603	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1603	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1604	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1604	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1604	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1605	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1607	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1608	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1608	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1608	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1609	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1609	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1609	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1610	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1610	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1611	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1612	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1614	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB1-1616	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0102	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0102	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0102	REFLPIVGHLGFQDS	6	21
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0103	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0103	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0104	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0108N	IREFLPIVGHLGFQD	5	20
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0108N	NIREFLPIVGHLGFQ	4	19
HYI-NFIA	chr1	43917319	chr1	61798184	821	DRB5-0108N	REFLPIVGHLGFQDS	6	21

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Fusion breakpoint peptide structures of HYI-NFIA

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
7774	REFLPIVGHLGFQD	HYI	NFIA	chr1	43917319	chr1	61798184	821

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of HYI-NFIA

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	7774	REFLPIVGHLGFQD	-7.2402	-7.2474
HLA-B52:01	3W39	7774	REFLPIVGHLGFQD	-6.34553	-6.35273
HLA-A11:01	4UQ2	7774	REFLPIVGHLGFQD	-6.91967	-6.92687
HLA-A24:02	5HGA	7774	REFLPIVGHLGFQD	-5.21987	-5.22707
HLA-B44:05	3DX8	7774	REFLPIVGHLGFQD	-2.70722	-2.71442

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Vaccine Design for the FusionNeoAntigens of HYI-NFIA

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
HYI-NFIA	chr1	43917319	chr1	61798184	12	22	VGHLGFQDSF	TTGGACATTTGGGCTTCCAGGACAGTTTTG
HYI-NFIA	chr1	43917319	chr1	61798184	5	15	IREFLPIVGH	TCCGGGAGTTCCTGCCCATTGTTGGACATT
HYI-NFIA	chr1	43917319	chr1	61798184	6	15	REFLPIVGH	GGGAGTTCCTGCCCATTGTTGGACATT
HYI-NFIA	chr1	43917319	chr1	61798184	6	16	REFLPIVGHL	GGGAGTTCCTGCCCATTGTTGGACATTTGG
HYI-NFIA	chr1	43917319	chr1	61798184	8	16	FLPIVGHL	TCCTGCCCATTGTTGGACATTTGG
HYI-NFIA	chr1	43917319	chr1	61798184	8	18	FLPIVGHLGF	TCCTGCCCATTGTTGGACATTTGGGCTTCC
HYI-NFIA	chr1	43917319	chr1	61798184	9	18	LPIVGHLGF	TGCCCATTGTTGGACATTTGGGCTTCC

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
HYI-NFIA	chr1	43917319	chr1	61798184	4	19	NIREFLPIVGHLGFQ	ACATCCGGGAGTTCCTGCCCATTGTTGGACATTTGGGCTTCCAGG
HYI-NFIA	chr1	43917319	chr1	61798184	5	20	IREFLPIVGHLGFQD	TCCGGGAGTTCCTGCCCATTGTTGGACATTTGGGCTTCCAGGACA
HYI-NFIA	chr1	43917319	chr1	61798184	6	21	REFLPIVGHLGFQDS	GGGAGTTCCTGCCCATTGTTGGACATTTGGGCTTCCAGGACAGTT

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Information of the samples that have these potential fusion neoantigens of HYI-NFIA

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
BRCA	HYI-NFIA	chr1	43917319	ENST00000372425	chr1	61798184	ENST00000371191	TCGA-OL-A5RZ-01A

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Potential target of CAR-T therapy development for HYI-NFIA

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 HYI-NFIA

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 HYI-NFIA

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)