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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:CHTOP-S100A1 (FusionGDB2 ID:16782)

Fusion Gene Summary for CHTOP-S100A1

Fusion gene summary

Fusion gene information	Fusion gene name: CHTOP-S100A1
	Fusion gene ID: 16782
		Hgene	Tgene
	Gene symbol	CHTOP	S100A1
	Gene ID	26097	6271
	Gene name	chromatin target of PRMT1	S100 calcium binding protein A1
	Synonyms	C10orf77\|C1orf77\|FL-SRAG\|FOP\|SRAG\|SRAG-3\|SRAG-5\|pp7704	S100\|S100-alpha\|S100A
	Cytomap	1q21.3	1q21.3
	Type of gene	protein-coding	protein-coding
	Description	chromatin target of PRMT1 proteinfriend of PRMT1 proteinsmall protein rich in arginine and glycine	protein S100-A1S-100 protein alpha chainS-100 protein subunit alphaS100 alphaS100 protein, alpha polypeptide
	Modification date	20200313	20200313
	UniProtAcc	Q9Y3Y2	.
	Ensembl transtripts involved in fusion gene	ENST00000368694, ENST00000495554, ENST00000403433, ENST00000368690, ENST00000368687, ENST00000368686,	ENST00000368698, ENST00000469893, ENST00000292169, ENST00000368696,
Fusion gene scores	* DoF score	7 X 8 X 5=280	3 X 5 X 3=45
	# samples	9	4
	** MAII score	log2(9/280*10)=-1.63742992061529 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/45*10)=-0.169925001442312 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CHTOP [Title/Abstract] AND S100A1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CHTOP(153606819)-S100A1(153602985), # samples:2
Anticipated loss of major functional domain due to fusion event.

* 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	CHTOP	GO:0006406	mRNA export from nucleus	23299939
Hgene	CHTOP	GO:0032781	positive regulation of ATPase activity	23299939
Hgene	CHTOP	GO:0051096	positive regulation of helicase activity	23299939
Tgene	S100A1	GO:0051000	positive regulation of nitric-oxide synthase activity	24244340
Tgene	S100A1	GO:1903672	positive regulation of sprouting angiogenesis	24244340

Fusion gene breakpoints across CHTOP (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 S100A1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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	UCS	TCGA-N8-A4PP	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
ChimerDB4	UCS	TCGA-N8-A4PP	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
ChimerDB4	UCS	TCGA-N8-A4PP-01A	CHTOP	chr1	153606819	-	S100A1	chr1	153602985	+
ChiTaRS5.0	N/A	AI830371	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+

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Fusion Gene ORF analysis for CHTOP-S100A1

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
5UTR-3CDS	ENST00000368694	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
5UTR-3UTR	ENST00000368694	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
5UTR-5UTR	ENST00000368694	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
5UTR-5UTR	ENST00000368694	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
3UTR-3CDS	ENST00000495554	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
3UTR-3UTR	ENST00000495554	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
3UTR-5UTR	ENST00000495554	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
3UTR-5UTR	ENST00000495554	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
5UTR-3CDS	ENST00000403433	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
5UTR-3UTR	ENST00000403433	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
5UTR-5UTR	ENST00000403433	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
5UTR-5UTR	ENST00000403433	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-3CDS	ENST00000368690	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-3UTR	ENST00000368690	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-5UTR	ENST00000368690	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-5UTR	ENST00000368690	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-3CDS	ENST00000368687	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-3UTR	ENST00000368687	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-5UTR	ENST00000368687	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-5UTR	ENST00000368687	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-3CDS	ENST00000368686	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-3UTR	ENST00000368686	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-5UTR	ENST00000368686	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
intron-5UTR	ENST00000368686	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153600903	+
5UTR-3CDS	ENST00000368694	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
5UTR-3UTR	ENST00000368694	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
5UTR-5UTR	ENST00000368694	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
5UTR-5UTR	ENST00000368694	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
3UTR-3CDS	ENST00000495554	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
3UTR-3UTR	ENST00000495554	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
3UTR-5UTR	ENST00000495554	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
3UTR-5UTR	ENST00000495554	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
5UTR-3CDS	ENST00000403433	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
5UTR-3UTR	ENST00000403433	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
5UTR-5UTR	ENST00000403433	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
5UTR-5UTR	ENST00000403433	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-3CDS	ENST00000368690	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-3UTR	ENST00000368690	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-5UTR	ENST00000368690	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-5UTR	ENST00000368690	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-3CDS	ENST00000368687	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-3UTR	ENST00000368687	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-5UTR	ENST00000368687	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-5UTR	ENST00000368687	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-3CDS	ENST00000368686	ENST00000368698	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-3UTR	ENST00000368686	ENST00000469893	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-5UTR	ENST00000368686	ENST00000292169	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
intron-5UTR	ENST00000368686	ENST00000368696	CHTOP	chr1	153606819	+	S100A1	chr1	153602985	+
5UTR-3CDS	ENST00000368694	ENST00000368698	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
5UTR-3UTR	ENST00000368694	ENST00000469893	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
5UTR-3UTR	ENST00000368694	ENST00000292169	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
5UTR-3UTR	ENST00000368694	ENST00000368696	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
3UTR-3CDS	ENST00000495554	ENST00000368698	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
3UTR-3UTR	ENST00000495554	ENST00000469893	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
3UTR-3UTR	ENST00000495554	ENST00000292169	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
3UTR-3UTR	ENST00000495554	ENST00000368696	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
5UTR-3CDS	ENST00000403433	ENST00000368698	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
5UTR-3UTR	ENST00000403433	ENST00000469893	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
5UTR-3UTR	ENST00000403433	ENST00000292169	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
5UTR-3UTR	ENST00000403433	ENST00000368696	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3CDS	ENST00000368690	ENST00000368698	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368690	ENST00000469893	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368690	ENST00000292169	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368690	ENST00000368696	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3CDS	ENST00000368687	ENST00000368698	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368687	ENST00000469893	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368687	ENST00000292169	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368687	ENST00000368696	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3CDS	ENST00000368686	ENST00000368698	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368686	ENST00000469893	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368686	ENST00000292169	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+
intron-3UTR	ENST00000368686	ENST00000368696	CHTOP	chr1	153606824	+	S100A1	chr1	153604213	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

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

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Fusion Genomic Features for CHTOP-S100A1

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
CHTOP	chr1	153606819	+	S100A1	chr1	153600897	+	0.3401887	0.65981126
CHTOP	chr1	153606819	+	S100A1	chr1	153602984	+	7.55E-06	0.9999925
CHTOP	chr1	153606819	+	S100A1	chr1	153600897	+	0.3401887	0.65981126
CHTOP	chr1	153606819	+	S100A1	chr1	153602984	+	7.55E-06	0.9999925

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for CHTOP-S100A1

Go to
FGviewer for the breakpoints of :-:
.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.

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

Hgene	Tgene
CHTOP Q9Y3Y2	.
FUNCTION: Plays an important role in the ligand-dependent activation of estrogen receptor target genes (PubMed:19858291). May play a role in the silencing of fetal globin genes (PubMed:20688955). Recruits the 5FMC complex to ZNF148, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes (By similarity). Plays an important role in the tumorigenicity of glioblastoma cells. Binds to 5-hydroxymethylcytosine (5hmC) and associates with the methylosome complex containing PRMT1, PRMT5, MEP50 and ERH. The CHTOP-methylosome complex associated with 5hmC is recruited to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of genes involved in glioblastomagenesis (PubMed:25284789). {ECO:0000250\|UniProtKB:Q9CY57, ECO:0000269\|PubMed:19858291, ECO:0000269\|PubMed:20688955, ECO:0000269\|PubMed:25284789}.; FUNCTION: Required for effective mRNA nuclear export and is a component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. Stimulates DDX39B ATPase and helicase activities. In cooperation with ALYREF/THOC4 enhances NXF1 RNA binding activity (PubMed:23299939). {ECO:0000269\|PubMed:23299939}.	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.

- In-frame and 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

- In-frame and 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

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Fusion Gene Sequence for CHTOP-S100A1

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CHTOP-S100A1

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for CHTOP-S100A1

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for CHTOP-S100A1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene	S100A1	C0265110	Cerebral Vasospasm	1	CTD_human
Tgene	S100A1	C0751895	Vasospasm, Intracranial	1	CTD_human