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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PAK1-INTS4 (FusionGDB2 ID:62014)

Fusion Gene Summary for PAK1-INTS4

check button Fusion gene summary
Fusion gene informationFusion gene name: PAK1-INTS4
Fusion gene ID: 62014
HgeneTgene
Gene symbol

PAK1

INTS4

Gene ID

5585

92105

Gene nameprotein kinase N1integrator complex subunit 4
SynonymsDBK|PAK-1|PAK1|PKN|PKN-ALPHA|PRK1|PRKCL1INT4|MST093
Cytomap

19p13.12

11q14.1

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase N1protease-activated kinase 1protein kinase C-like 1protein kinase C-like PKNprotein kinase C-related kinase 1protein kinase PKN-alphaserine-threonine kinase Nserine/threonine protein kinase Nintegrator complex subunit 4MSTP093
Modification date2020032920200313
UniProtAcc.

Q96HW7

Ensembl transtripts involved in fusion geneENST00000356341, ENST00000530617, 
ENST00000278568, ENST00000528203, 
ENST00000525542, 		ENST00000534064, 
ENST00000535943, ENST00000525931, 
ENST00000529807, ENST00000527522, 
Fusion gene scores* DoF score31 X 18 X 9=502213 X 9 X 8=936
# samples 3616
** MAII scorelog2(36/5022*10)=-3.80219321694183
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/936*10)=-2.54843662469604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PAK1 [Title/Abstract] AND INTS4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPAK1(77184596)-INTS4(77618856), # samples:1
PAK1(77184597)-INTS4(77618856), # samples:1
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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePAK1

GO:0006357

regulation of transcription by RNA polymerase II

12514133

HgenePAK1

GO:0006468

protein phosphorylation

17332740

HgenePAK1

GO:0035407

histone H3-T11 phosphorylation

18066052

TgeneINTS4

GO:0016180

snRNA processing

16239144


check buttonFusion gene breakpoints across PAK1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across INTS4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4STADTCGA-CD-5800PAK1chr11

77184596

-INTS4chr11

77618856

-
ChimerDB4STADTCGA-CD-5800-01APAK1chr11

77184597

-INTS4chr11

77618856

-


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Fusion Gene ORF analysis for PAK1-INTS4

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5UTR-3CDSENST00000356341ENST00000534064PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-3CDSENST00000356341ENST00000535943PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-intronENST00000356341ENST00000525931PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-intronENST00000356341ENST00000529807PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-intronENST00000356341ENST00000527522PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-3CDSENST00000530617ENST00000534064PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-3CDSENST00000530617ENST00000535943PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000530617ENST00000525931PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000530617ENST00000529807PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000530617ENST00000527522PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-3CDSENST00000278568ENST00000534064PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-3CDSENST00000278568ENST00000535943PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-intronENST00000278568ENST00000525931PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-intronENST00000278568ENST00000529807PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-intronENST00000278568ENST00000527522PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-3CDSENST00000528203ENST00000534064PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-3CDSENST00000528203ENST00000535943PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000528203ENST00000525931PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000528203ENST00000529807PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000528203ENST00000527522PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-3CDSENST00000525542ENST00000534064PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-3CDSENST00000525542ENST00000535943PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000525542ENST00000525931PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000525542ENST00000529807PAK1chr11

77184596

-INTS4chr11

77618856

-
intron-intronENST00000525542ENST00000527522PAK1chr11

77184596

-INTS4chr11

77618856

-
5UTR-3CDSENST00000356341ENST00000534064PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-3CDSENST00000356341ENST00000535943PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-intronENST00000356341ENST00000525931PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-intronENST00000356341ENST00000529807PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-intronENST00000356341ENST00000527522PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-3CDSENST00000530617ENST00000534064PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-3CDSENST00000530617ENST00000535943PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000530617ENST00000525931PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000530617ENST00000529807PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000530617ENST00000527522PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-3CDSENST00000278568ENST00000534064PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-3CDSENST00000278568ENST00000535943PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-intronENST00000278568ENST00000525931PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-intronENST00000278568ENST00000529807PAK1chr11

77184597

-INTS4chr11

77618856

-
5UTR-intronENST00000278568ENST00000527522PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-3CDSENST00000528203ENST00000534064PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-3CDSENST00000528203ENST00000535943PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000528203ENST00000525931PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000528203ENST00000529807PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000528203ENST00000527522PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-3CDSENST00000525542ENST00000534064PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-3CDSENST00000525542ENST00000535943PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000525542ENST00000525931PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000525542ENST00000529807PAK1chr11

77184597

-INTS4chr11

77618856

-
intron-intronENST00000525542ENST00000527522PAK1chr11

77184597

-INTS4chr11

77618856

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for PAK1-INTS4


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution 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.

check buttonDistribution 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 PAK1-INTS4


check button 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.INTS4

Q96HW7

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.FUNCTION: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for PAK1-INTS4


check button 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 PAK1-INTS4


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for PAK1-INTS4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for PAK1-INTS4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePAK1C4748428INTELLECTUAL DEVELOPMENTAL DISORDER WITH MACROCEPHALY, SEIZURES, AND SPEECH DELAY2GENOMICS_ENGLAND;UNIPROT
HgenePAK1C0006142Malignant neoplasm of breast1CTD_human
HgenePAK1C0007134Renal Cell Carcinoma1CTD_human
HgenePAK1C0033687Proteinuria1CTD_human
HgenePAK1C0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
HgenePAK1C0678222Breast Carcinoma1CTD_human
HgenePAK1C1257931Mammary Neoplasms, Human1CTD_human
HgenePAK1C1266042Chromophobe Renal Cell Carcinoma1CTD_human
HgenePAK1C1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
HgenePAK1C1266044Collecting Duct Carcinoma of the Kidney1CTD_human
HgenePAK1C1306837Papillary Renal Cell Carcinoma1CTD_human
HgenePAK1C1458155Mammary Neoplasms1CTD_human
HgenePAK1C1535926Neurodevelopmental Disorders1GENOMICS_ENGLAND
HgenePAK1C4704874Mammary Carcinoma, Human1CTD_human
TgeneINTS4C0033578Prostatic Neoplasms1CTD_human
TgeneINTS4C0376358Malignant neoplasm of prostate1CTD_human