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Fusion gene ID: 29436

FusionGeneSummary for PTPN1_ROMO1

Fusion gene summary

Fusion gene information	Fusion gene name: PTPN1_ROMO1
	Fusion gene ID: 29436
		Hgene	Tgene
	Gene symbol	PTPN1	ROMO1
	Gene ID	5770	140823
	Gene name	protein tyrosine phosphatase, non-receptor type 1	reactive oxygen species modulator 1
	Synonyms	PTP1B	C20orf52\|MTGM\|MTGMP\|bA353C18.2
	Cytomap	20q13.13	20q11.22
	Type of gene	protein-coding	protein-coding
	Description	tyrosine-protein phosphatase non-receptor type 1protein tyrosine phosphatase, placentalprotein-tyrosine phosphatase 1B	reactive oxygen species modulator 1PCM19ROS modulator 1epididymis tissue protein Li 175glyrichinmitochondrial targeting GXXXG proteinmitochondrial targeting GxxxG motif proteinprotein MGR2 homolog
	Modification date	20180522	20180523
	UniProtAcc	P18031	P60602
	Ensembl transtripts involved in fusion gene	ENST00000371621, ENST00000541713,	ENST00000374078, ENST00000374077, ENST00000374072, ENST00000397416, ENST00000336695,
Fusion gene scores	* DoF score	7 X 4 X 5=140	5 X 5 X 3=75
	# samples	8	5
	** MAII score	log2(8/140*10)=-0.807354922057604 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/75*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: PTPN1 [Title/Abstract] AND ROMO1 [Title/Abstract] AND fusion [Title/Abstract]
Functional or gene categories assigned by FusionGDB annotation	Tumor suppressor gene involved fusion gene, in-frame but not retained their domain.

* 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	PTPN1	GO:0030100	regulation of endocytosis	21135139
Hgene	PTPN1	GO:0030968	endoplasmic reticulum unfolded protein response	22169477
Hgene	PTPN1	GO:0035335	peptidyl-tyrosine dephosphorylation	21135139
Hgene	PTPN1	GO:0061098	positive regulation of protein tyrosine kinase activity	21216966
Hgene	PTPN1	GO:1903898	negative regulation of PERK-mediated unfolded protein response	21216966
Tgene	ROMO1	GO:0008284	positive regulation of cell proliferation	18313394
Tgene	ROMO1	GO:0031640	killing of cells of other organism	22083756
Tgene	ROMO1	GO:0042742	defense response to bacterium	22083756
Tgene	ROMO1	GO:0050829	defense response to Gram-negative bacterium	22083756
Tgene	ROMO1	GO:0050830	defense response to Gram-positive bacterium	22083756
Tgene	ROMO1	GO:0051715	cytolysis in other organism	22083756
Tgene	ROMO1	GO:2000379	positive regulation of reactive oxygen species metabolic process	16842742

Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.

Data type	Source	Cancer type	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
TCGA	LD	BRCA	TCGA-EW-A2FW-01A	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+

* LD: Li Ding group's fusion gene list
RV: Roel Verhaak group's fusion gene list
ChiTaRs fusion database

Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
In-frame	ENST00000371621	ENST00000374078	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
In-frame	ENST00000371621	ENST00000374077	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
In-frame	ENST00000371621	ENST00000374072	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
In-frame	ENST00000371621	ENST00000397416	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
Frame-shift	ENST00000371621	ENST00000336695	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
In-frame	ENST00000541713	ENST00000374078	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
In-frame	ENST00000541713	ENST00000374077	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
In-frame	ENST00000541713	ENST00000374072	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
In-frame	ENST00000541713	ENST00000397416	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+
Frame-shift	ENST00000541713	ENST00000336695	PTPN1	chr20	49191191	+	ROMO1	chr20	34287555	+

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FusionProtFeatures for PTPN1_ROMO1

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

Hgene	Tgene
PTPN1 P18031	ROMO1 P60602

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Fusion gene ID: 29436

FusionGeneSummary for PTPN1_ROMO1

FusionProtFeatures for PTPN1_ROMO1