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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:PID1-MRPS6

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PID1-MRPS6
	FusionPDB ID: 65184
	FusionGDB2.0 ID: 65184
		Hgene	Tgene
	Gene symbol	PID1	MRPS6
	Gene ID	55022	64968
	Gene name	phosphotyrosine interaction domain containing 1	mitochondrial ribosomal protein S6
	Synonyms	HMFN2073\|NYGGF4\|P-CLI1\|PCLI1	C21orf101\|MRP-S6\|RPMS6\|S6mt
	Cytomap	2q36.3	21q22.11
	Type of gene	protein-coding	protein-coding
	Description	PTB-containing, cubilin and LRP1-interacting proteinphosphotyrosine interaction domain-containing protein 1	28S ribosomal protein S6, mitochondrialmitochondrial small ribosomal subunit protein bS6m
	Modification date	20200313	20200313
	UniProtAcc	.	P82932
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000354069, ENST00000392054, ENST00000392055, ENST00000409462, ENST00000482518,	ENST00000482679, ENST00000399312,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 9 X 4=324	13 X 6 X 7=546
	# samples	10	15
	** MAII score	log2(10/324*10)=-1.6959938131099 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/546*10)=-1.86393845042397 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PID1 [Title/Abstract] AND MRPS6 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PID1(230020534)-MRPS6(35497641), # samples:4
Anticipated loss of major functional domain due to fusion event.	PID1-MRPS6 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. PID1-MRPS6 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. PID1-MRPS6 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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	PID1	GO:0001933	negative regulation of protein phosphorylation	19079291
Hgene	PID1	GO:0045444	fat cell differentiation	16815647
Hgene	PID1	GO:0046325	negative regulation of glucose import	19079291
Hgene	PID1	GO:0046627	negative regulation of insulin receptor signaling pathway	19079291
Hgene	PID1	GO:0070346	positive regulation of fat cell proliferation	16815647
Hgene	PID1	GO:1903077	negative regulation of protein localization to plasma membrane	19079291

Fusion gene breakpoints across PID1 (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 MRPS6 (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 Gene Sample Information

Fusion gene information from FusionGDB2.0.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	SARC	TCGA-3B-A9HT-01A	PID1	chr2	230020534	-	MRPS6	chr21	35497641	+
ChimerDB4	SARC	TCGA-DX-A3U7-01A	PID1	chr2	230020534	-	MRPS6	chr21	35497641	+
ChimerDB4	SARC	TCGA-DX-A3U7	PID1	chr2	230020533	-	MRPS6	chr21	35497640	+
ChimerDB4	SARC	TCGA-DX-A3U7	PID1	chr2	230020533	-	MRPS6	chr21	35514707	+
ChimerDB4	SARC	TCGA-DX-A3U7	PID1	chr2	230135729	-	MRPS6	chr21	35497640	+

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Fusion ORF Analysis

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)
ENST00000392055	PID1	chr2	230020534	-	ENST00000399312	MRPS6	chr21	35497641	+	1186	419	80	751	223
ENST00000354069	PID1	chr2	230020534	-	ENST00000399312	MRPS6	chr21	35497641	+	1074	307	10	639	209
ENST00000392055	PID1	chr2	230020533	-	ENST00000399312	MRPS6	chr21	35497640	+	1186	419	80	751	223
ENST00000354069	PID1	chr2	230020533	-	ENST00000399312	MRPS6	chr21	35497640	+	1074	307	10	639	209
ENST00000392054	PID1	chr2	230020533	-	ENST00000399312	MRPS6	chr21	35514707	+	1237	610	199	651	150
ENST00000409462	PID1	chr2	230135729	-	ENST00000399312	MRPS6	chr21	35497640	+	1034	267	75	599	174
ENST00000392055	PID1	chr2	230135729	-	ENST00000399312	MRPS6	chr21	35497640	+	1039	272	80	604	174

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
ENST00000392055	ENST00000399312	PID1	chr2	230020534	-	MRPS6	chr21	35497641	+	0.006955158	0.9930448
ENST00000354069	ENST00000399312	PID1	chr2	230020534	-	MRPS6	chr21	35497641	+	0.004075023	0.99592495
ENST00000392055	ENST00000399312	PID1	chr2	230020533	-	MRPS6	chr21	35497640	+	0.006955158	0.9930448
ENST00000354069	ENST00000399312	PID1	chr2	230020533	-	MRPS6	chr21	35497640	+	0.004075023	0.99592495
ENST00000392054	ENST00000399312	PID1	chr2	230020533	-	MRPS6	chr21	35514707	+	0.48723483	0.5127652
ENST00000409462	ENST00000399312	PID1	chr2	230135729	-	MRPS6	chr21	35497640	+	0.030526938	0.96947306
ENST00000392055	ENST00000399312	PID1	chr2	230135729	-	MRPS6	chr21	35497640	+	0.02013042	0.9798696

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>65184_65184_1_PID1-MRPS6_PID1_chr2_230020533_ENST00000354069_MRPS6_chr21_35497640_ENST00000399312_length(amino acids)=209AA_BP=99
MYKRLRAMFSLPLSLPLCEDTAFLPSKCCSSHKTIKQARTLIMIFLASGTHFQTMLKSKLNVLTLKKEPLPAVIFHEPEAIELCTTTPLM
KTRTHSGCKPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNRGGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKH

--------------------------------------------------------------

>65184_65184_2_PID1-MRPS6_PID1_chr2_230020533_ENST00000392054_MRPS6_chr21_35514707_ENST00000399312_length(amino acids)=150AA_BP=
MPKPRAGRCGSRPRSACRRDLQTQKRHREGHCEDQGRNRSYGIISQGMPRIAGNHLMLEESRTCSSPELLDGVWPCQPLHFGLPASEMHF

--------------------------------------------------------------

>65184_65184_3_PID1-MRPS6_PID1_chr2_230020533_ENST00000392055_MRPS6_chr21_35497640_ENST00000399312_length(amino acids)=223AA_BP=113
MLAAPYAHPAAVASARTHIPRTPTPDVKRDPSPSPPGAIDSLASVSSAKTQGWKMWQPATERLQHFQTMLKSKLNVLTLKKEPLPAVIFH
EPEAIELCTTTPLMKTRTHSGCKPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNRGGYFLVDFYAPTAAVESMVEHL

--------------------------------------------------------------

>65184_65184_4_PID1-MRPS6_PID1_chr2_230020534_ENST00000354069_MRPS6_chr21_35497641_ENST00000399312_length(amino acids)=209AA_BP=99
MYKRLRAMFSLPLSLPLCEDTAFLPSKCCSSHKTIKQARTLIMIFLASGTHFQTMLKSKLNVLTLKKEPLPAVIFHEPEAIELCTTTPLM
KTRTHSGCKPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNRGGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKH

--------------------------------------------------------------

>65184_65184_5_PID1-MRPS6_PID1_chr2_230020534_ENST00000392055_MRPS6_chr21_35497641_ENST00000399312_length(amino acids)=223AA_BP=113
MLAAPYAHPAAVASARTHIPRTPTPDVKRDPSPSPPGAIDSLASVSSAKTQGWKMWQPATERLQHFQTMLKSKLNVLTLKKEPLPAVIFH
EPEAIELCTTTPLMKTRTHSGCKPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNRGGYFLVDFYAPTAAVESMVEHL

--------------------------------------------------------------

>65184_65184_6_PID1-MRPS6_PID1_chr2_230135729_ENST00000392055_MRPS6_chr21_35497640_ENST00000399312_length(amino acids)=174AA_BP=63
MLAAPYAHPAAVASARTHIPRTPTPDVKRDPSPSPPGAIDSLASVSSAKTQGWKMWQPATERLQPETAATLKRTIEALMDRGAIVRDLEN

--------------------------------------------------------------

>65184_65184_7_PID1-MRPS6_PID1_chr2_230135729_ENST00000409462_MRPS6_chr21_35497640_ENST00000399312_length(amino acids)=174AA_BP=63
MLAAPYAHPAAVASARTHIPRTPTPDVKRDPSPSPPGAIDSLASVSSAKTQGWKMWQPATERLQPETAATLKRTIEALMDRGAIVRDLEN

--------------------------------------------------------------

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:230020534/chr21:35497641)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	MRPS6 P82932
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

PID1

chr2:230020533

chr21:35497640

ENST00000354069

93_250

92.0

251.0

Domain

PID

Hgene

PID1

chr2:230020533

chr21:35497640

ENST00000392054

93_250

90.0

249.0

Domain

PID

Hgene

PID1

chr2:230020533

chr21:35497640

ENST00000392055

93_250

59.0

218.0

Domain

PID

Hgene

PID1

chr2:230020533

chr21:35497640

ENST00000409462

93_250

169.0

Domain

PID

Hgene

PID1

chr2:230020533

chr21:35514707

ENST00000354069

93_250

92.0

251.0

Domain

PID

Hgene

PID1

chr2:230020533

chr21:35514707

ENST00000392054

93_250

90.0

249.0

Domain

PID

Hgene

PID1

chr2:230020533

chr21:35514707

ENST00000392055

93_250

59.0

218.0

Domain

PID

Hgene

PID1

chr2:230020533

chr21:35514707

ENST00000409462

93_250

169.0

Domain

PID

Hgene

PID1

chr2:230020534

chr21:35497641

ENST00000354069

93_250

92.0

251.0

Domain

PID

Hgene

PID1

chr2:230020534

chr21:35497641

ENST00000392054

93_250

90.0

249.0

Domain

PID

Hgene

PID1

chr2:230020534

chr21:35497641

ENST00000392055

93_250

59.0

218.0

Domain

PID

Hgene

PID1

chr2:230020534

chr21:35497641

ENST00000409462

93_250

169.0

Domain

PID

Hgene

PID1

chr2:230135729

chr21:35497640

ENST00000354069

93_250

251.0

Domain

PID

Hgene

PID1

chr2:230135729

chr21:35497640

ENST00000392054

93_250

249.0

Domain

PID

Hgene

PID1

chr2:230135729

chr21:35497640

ENST00000392055

93_250

10.0

218.0

Domain

PID

Hgene

PID1

chr2:230135729

chr21:35497640

ENST00000409462

93_250

10.0

169.0

Domain

PID

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>333_PID1_230020534_MRPS6_35497641_ranked_0.pdb	PID1	230135729	230020534	ENST00000399312	MRPS6	chr21	35497641	+	MLAAPYAHPAAVASARTHIPRTPTPDVKRDPSPSPPGAIDSLASVSSAKTQGWKMWQPATERLQHFQTMLKSKLNVLTLKKEPLPAVIFH EPEAIELCTTTPLMKTRTHSGCKPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNRGGYFLVDFYAPTAAVESMVEHL	223

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

PID1_pLDDT.png

MRPS6_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
PID1
MRPS6

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to PID1-MRPS6

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 PID1-MRPS6

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