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Fusion Protein:PPIC-TRPM7

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PPIC-TRPM7
	FusionPDB ID: 67529
	FusionGDB2.0 ID: 67529
		Hgene	Tgene
	Gene symbol	PPIC	TRPM7
	Gene ID	5480	54822
	Gene name	peptidylprolyl isomerase C	transient receptor potential cation channel subfamily M member 7
	Synonyms	CYPC	ALSPDC\|CHAK\|CHAK1\|LTRPC7\|LTrpC-7\|TRP-PLIK
	Cytomap	5q23.2	15q21.2
	Type of gene	protein-coding	protein-coding
	Description	peptidyl-prolyl cis-trans isomerase CPPIase Ccyclophilin Cparvulinrotamase C	transient receptor potential cation channel subfamily M member 7LTRPC ion channel family member 7channel-kinase 1long transient receptor potential channel 7transient receptor potential-phospholipase C-interacting kinase
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000306442,	ENST00000561443, ENST00000313478, ENST00000560955,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 2=18	13 X 16 X 5=1040
	# samples	3	15
	** MAII score	log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(15/1040*10)=-2.79354912253257 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PPIC [Title/Abstract] AND TRPM7 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PPIC [Title/Abstract] AND TRPM7 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PPIC(122365000)-TRPM7(50905026), # samples:1
Anticipated loss of major functional domain due to fusion event.	PPIC-TRPM7 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. PPIC-TRPM7 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. PPIC-TRPM7 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. PPIC-TRPM7 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	PPIC	GO:0000413	protein peptidyl-prolyl isomerization	20676357

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:122365000/chr15:50905026)
- 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 PPIC (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 TRPM7 (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)
ENST00000306442	PPIC	chr5	122365000	-	ENST00000560955	TRPM7	chr15	50905026	-	5557	347	101	4171	1356
ENST00000306442	PPIC	chr5	122365000	-	ENST00000313478	TRPM7	chr15	50905026	-	5558	347	101	4174	1357

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
ENST00000306442	ENST00000560955	PPIC	chr5	122365000	-	TRPM7	chr15	50905026	-	0.000157978	0.99984205
ENST00000306442	ENST00000313478	PPIC	chr5	122365000	-	TRPM7	chr15	50905026	-	0.00011464	0.9998853

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 PPIC-TRPM7

+/-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
PPIC	chr5	122365000	TRPM7	chr15	50905026	347	82	KTVENFVALATGEIDTVMEEGKKKRT

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Potential FusionNeoAntigen Information of PPIC-TRPM7 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.

PPIC-TRPM7_122365000_50905026.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)
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:22	ALATGEIDTV	0.9972	0.7448	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:27	ALATGEIDTV	0.9942	0.7595	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:13	ALATGEIDTV	0.9934	0.8144	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:30	ALATGEIDTV	0.9909	0.6948	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:67	ALATGEIDTV	0.9909	0.6948	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:60	ALATGEIDTV	0.9909	0.6991	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:24	ALATGEIDTV	0.9909	0.6948	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:16	ALATGEIDTV	0.9896	0.6911	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:38	ALATGEIDTV	0.9812	0.8196	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:19	ALATGEIDTV	0.9747	0.5963	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:35	ALATGEIDTV	0.9084	0.7281	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:29	ALATGEIDTV	0.8834	0.7061	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:20	ALATGEIDTV	0.8682	0.7014	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:02	ALATGEIDTV	0.9973	0.6451	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:01	ALATGEIDTV	0.9909	0.6948	7	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-B51:05	LATGEIDTV	0.7593	0.5556	8	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	HLA-A02:03	ALATGEIDTV	0.9973	0.7707	7	17

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Potential FusionNeoAntigen Information of PPIC-TRPM7 in HLA II

PPIC-TRPM7_122365000_50905026.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)
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0101	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0101	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0105	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0105	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0107	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0107	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0109	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0111	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0111	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0113	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0113	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0115	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0115	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0117	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0117	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0117	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0119	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0119	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0121	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0121	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0125	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0125	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0127	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0127	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0129	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0129	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0129	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0131	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0131	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0447	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0447	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0469	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0469	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0482	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0482	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0482	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0807	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0807	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0807	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0819	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0819	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0819	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0825	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0825	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0825	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0832	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0832	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0834	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0834	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0834	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0905	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-0905	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1001	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1001	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1003	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1003	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1216	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1216	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1216	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1216	ENFVALATGEIDTVM	3	18
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1222	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1222	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1222	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-13100	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-13100	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1346	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1346	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1446	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1446	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1448	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1448	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1527	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1527	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1534	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1534	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1601	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1601	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1601	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1601	ENFVALATGEIDTVM	3	18
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1602	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1602	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1602	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1603	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1603	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1603	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1603	ENFVALATGEIDTVM	3	18
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1604	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1604	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1604	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1605	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1605	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1607	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1607	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1608	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1608	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1608	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1608	ENFVALATGEIDTVM	3	18
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1609	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1609	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1609	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1609	ENFVALATGEIDTVM	3	18
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1610	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1610	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1610	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1611	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1611	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1611	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1612	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1612	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1612	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1614	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1614	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1614	KTVENFVALATGEID	0	15
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1616	VENFVALATGEIDTV	2	17
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1616	TVENFVALATGEIDT	1	16
PPIC-TRPM7	chr5	122365000	chr15	50905026	347	DRB1-1616	KTVENFVALATGEID	0	15

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Fusion breakpoint peptide structures of PPIC-TRPM7

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
9792	VALATGEIDTVMEE	PPIC	TRPM7	chr5	122365000	chr15	50905026	347

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PPIC-TRPM7

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	9792	VALATGEIDTVMEE	-7.9962	-8.1096
HLA-B14:02	3BVN	9792	VALATGEIDTVMEE	-5.70842	-6.74372
HLA-B52:01	3W39	9792	VALATGEIDTVMEE	-6.83737	-6.95077
HLA-B52:01	3W39	9792	VALATGEIDTVMEE	-4.4836	-5.5189
HLA-A11:01	4UQ2	9792	VALATGEIDTVMEE	-10.0067	-10.1201
HLA-A11:01	4UQ2	9792	VALATGEIDTVMEE	-9.03915	-10.0745
HLA-A24:02	5HGA	9792	VALATGEIDTVMEE	-6.56204	-6.67544
HLA-A24:02	5HGA	9792	VALATGEIDTVMEE	-5.42271	-6.45801
HLA-B44:05	3DX8	9792	VALATGEIDTVMEE	-7.85648	-8.89178
HLA-B44:05	3DX8	9792	VALATGEIDTVMEE	-5.3978	-5.5112
HLA-A02:01	6TDR	9792	VALATGEIDTVMEE	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of PPIC-TRPM7

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
PPIC-TRPM7	chr5	122365000	chr15	50905026	7	17	ALATGEIDTV	GCTCTAGCAACAGGAGAGATTGATACAGTT
PPIC-TRPM7	chr5	122365000	chr15	50905026	8	17	LATGEIDTV	CTAGCAACAGGAGAGATTGATACAGTT

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
PPIC-TRPM7	chr5	122365000	chr15	50905026	0	15	KTVENFVALATGEID	AAGACAGTGGAAAATTTTGTTGCTCTAGCAACAGGAGAGATTGAT
PPIC-TRPM7	chr5	122365000	chr15	50905026	1	16	TVENFVALATGEIDT	ACAGTGGAAAATTTTGTTGCTCTAGCAACAGGAGAGATTGATACA
PPIC-TRPM7	chr5	122365000	chr15	50905026	2	17	VENFVALATGEIDTV	GTGGAAAATTTTGTTGCTCTAGCAACAGGAGAGATTGATACAGTT
PPIC-TRPM7	chr5	122365000	chr15	50905026	3	18	ENFVALATGEIDTVM	GAAAATTTTGTTGCTCTAGCAACAGGAGAGATTGATACAGTTATG

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Information of the samples that have these potential fusion neoantigens of PPIC-TRPM7

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
STAD	PPIC-TRPM7	chr5	122365000	ENST00000306442	chr15	50905026	ENST00000313478	TCGA-HU-A4GH-01A

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Potential target of CAR-T therapy development for PPIC-TRPM7

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

TRPM7

chr5:122365000

chr15:50905026

ENST00000313478

1036_1056

1866.0

Intramembrane

Pore-forming

Tgene

TRPM7

chr5:122365000

chr15:50905026

ENST00000313478

1075_1095

1866.0

Transmembrane

Helical

Tgene

TRPM7

chr5:122365000

chr15:50905026

ENST00000313478

756_776

1866.0

Transmembrane

Helical

Tgene

TRPM7

chr5:122365000

chr15:50905026

ENST00000313478

856_876

1866.0

Transmembrane

Helical

Tgene

TRPM7

chr5:122365000

chr15:50905026

ENST00000313478

919_939

1866.0

Transmembrane

Helical

Tgene

TRPM7

chr5:122365000

chr15:50905026

ENST00000313478

963_983

1866.0

Transmembrane

Helical

Tgene

TRPM7

chr5:122365000

chr15:50905026

ENST00000313478

996_1016

1866.0

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 PPIC-TRPM7

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 PPIC-TRPM7

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)