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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:ARHGEF10L-PAK4 (FusionGDB2 ID:6185)

Fusion Gene Summary for ARHGEF10L-PAK4

Fusion gene summary

Fusion gene information	Fusion gene name: ARHGEF10L-PAK4
	Fusion gene ID: 6185
		Hgene	Tgene
	Gene symbol	ARHGEF10L	PAK4
	Gene ID	55160	10298
	Gene name	Rho guanine nucleotide exchange factor 10 like	p21 (RAC1) activated kinase 4
	Synonyms	GrinchGEF	-
	Cytomap	1p36.13	19q13.2
	Type of gene	protein-coding	protein-coding
	Description	rho guanine nucleotide exchange factor 10-like proteinRho guanine nucleotide exchange factor (GEF) 10-like	serine/threonine-protein kinase PAK 4p21 protein (Cdc42/Rac)-activated kinase 4p21(CDKN1A)-activated kinase 4protein kinase related to S. cerevisiae STE20, effector for Cdc42Hs
	Modification date	20200313	20200313
	UniProtAcc	Q9HCE6	C3orf54,FAM212A
	Ensembl transtripts involved in fusion gene	ENST00000469726, ENST00000167825, ENST00000361221, ENST00000375408, ENST00000375415, ENST00000434513, ENST00000452522, ENST00000375420,	ENST00000321944, ENST00000358301, ENST00000360442, ENST00000435673, ENST00000593690, ENST00000599386, ENST00000599470, ENST00000597766,
Fusion gene scores	* DoF score	12 X 12 X 12=1728	8 X 8 X 3=192
	# samples	17	9
	** MAII score	log2(17/1728*10)=-3.34549656602577 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/192*10)=-1.09310940439148 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: ARHGEF10L [Title/Abstract] AND PAK4 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	ARHGEF10L(17991090)-PAK4(39660172), # 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	ARHGEF10L	GO:0032933	SREBP signaling pathway	16112081
Hgene	ARHGEF10L	GO:0051496	positive regulation of stress fiber assembly	16112081

Fusion gene breakpoints across ARHGEF10L (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 PAK4 (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	STAD	TCGA-CG-4449-01A	ARHGEF10L	chr1	17991090	-	PAK4	chr19	39660172	+
ChimerDB4	STAD	TCGA-CG-4449-01A	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+

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Fusion Gene ORF analysis for ARHGEF10L-PAK4

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
3UTR-5UTR	ENST00000469726	ENST00000321944	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
3UTR-5UTR	ENST00000469726	ENST00000358301	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
3UTR-5UTR	ENST00000469726	ENST00000360442	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
3UTR-5UTR	ENST00000469726	ENST00000435673	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
3UTR-5UTR	ENST00000469726	ENST00000593690	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
3UTR-5UTR	ENST00000469726	ENST00000599386	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
3UTR-5UTR	ENST00000469726	ENST00000599470	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
3UTR-intron	ENST00000469726	ENST00000597766	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000167825	ENST00000321944	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000167825	ENST00000358301	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000167825	ENST00000360442	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000167825	ENST00000435673	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000167825	ENST00000593690	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000167825	ENST00000599386	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000167825	ENST00000599470	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000361221	ENST00000321944	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000361221	ENST00000358301	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000361221	ENST00000360442	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000361221	ENST00000435673	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000361221	ENST00000593690	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000361221	ENST00000599386	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000361221	ENST00000599470	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375408	ENST00000321944	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375408	ENST00000358301	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375408	ENST00000360442	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375408	ENST00000435673	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375408	ENST00000593690	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375408	ENST00000599386	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375408	ENST00000599470	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375415	ENST00000321944	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375415	ENST00000358301	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375415	ENST00000360442	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375415	ENST00000435673	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375415	ENST00000593690	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375415	ENST00000599386	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000375415	ENST00000599470	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000434513	ENST00000321944	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000434513	ENST00000358301	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000434513	ENST00000360442	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000434513	ENST00000435673	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000434513	ENST00000593690	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000434513	ENST00000599386	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000434513	ENST00000599470	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000452522	ENST00000321944	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000452522	ENST00000358301	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000452522	ENST00000360442	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000452522	ENST00000435673	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000452522	ENST00000593690	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000452522	ENST00000599386	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-5UTR	ENST00000452522	ENST00000599470	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-intron	ENST00000167825	ENST00000597766	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-intron	ENST00000361221	ENST00000597766	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-intron	ENST00000375408	ENST00000597766	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-intron	ENST00000375415	ENST00000597766	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-intron	ENST00000434513	ENST00000597766	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
5CDS-intron	ENST00000452522	ENST00000597766	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
intron-5UTR	ENST00000375420	ENST00000321944	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
intron-5UTR	ENST00000375420	ENST00000358301	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
intron-5UTR	ENST00000375420	ENST00000360442	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
intron-5UTR	ENST00000375420	ENST00000435673	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
intron-5UTR	ENST00000375420	ENST00000593690	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
intron-5UTR	ENST00000375420	ENST00000599386	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
intron-5UTR	ENST00000375420	ENST00000599470	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+
intron-intron	ENST00000375420	ENST00000597766	ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660172	+

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 ARHGEF10L-PAK4

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)
ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660171	+	3.45E-07	0.99999964
ARHGEF10L	chr1	17991090	+	PAK4	chr19	39660171	+	3.45E-07	0.99999964

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 ARHGEF10L-PAK4

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:17991090/:39660172)
- 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
ARHGEF10L Q9HCE6	PAK4 C3orf54,FAM212A
FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RHOA, RHOB and RHOC. {ECO:0000269\|PubMed:16112081}.	287

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 ARHGEF10L-PAK4

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 ARHGEF10L-PAK4

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 ARHGEF10L-PAK4

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 ARHGEF10L-PAK4

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source