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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:KRT18-PKM (FusionGDB2 ID:43315)

Fusion Gene Summary for KRT18-PKM

check button Fusion gene summary
Fusion gene informationFusion gene name: KRT18-PKM
Fusion gene ID: 43315
HgeneTgene
Gene symbol

KRT18

PKM

Gene ID

3875

5315

Gene namekeratin 18pyruvate kinase M1/2
SynonymsCK-18|CYK18|K18CTHBP|HEL-S-30|OIP3|PK3|PKM2|TCB|THBP1|p58
Cytomap

12q13.13

15q23

Type of geneprotein-codingprotein-coding
Descriptionkeratin, type I cytoskeletal 18cell proliferation-inducing gene 46 proteincytokeratin 18keratin 18, type Ipyruvate kinase PKMOPA-interacting protein 3PK, muscle typecytosolic thyroid hormone-binding proteinepididymis secretory protein Li 30pyruvate kinase 2/3pyruvate kinase isozymes M1/M2pyruvate kinase muscle isozymepyruvate kinase, musclethyroid ho
Modification date2020032720200329
UniProtAcc

P05783

Q99640

Ensembl transtripts involved in fusion geneENST00000388837, ENST00000550600, 
ENST00000388835, 		ENST00000319622, 
ENST00000565184, ENST00000389093, 
ENST00000335181, ENST00000568883, 
ENST00000449901, ENST00000565154, 
ENST00000568459, 
Fusion gene scores* DoF score4 X 5 X 1=2034 X 37 X 9=11322
# samples 541
** MAII scorelog2(5/20*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(41/11322*10)=-4.78736110881616
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KRT18 [Title/Abstract] AND PKM [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKRT18(53343622)-PKM(72499549), # 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
HgeneKRT18

GO:0043000

Golgi to plasma membrane CFTR protein transport

15529338

HgeneKRT18

GO:0043066

negative regulation of apoptotic process

11684708

HgeneKRT18

GO:0045104

intermediate filament cytoskeleton organization

20346438

TgenePKM

GO:0012501

programmed cell death

17308100


check buttonFusion gene breakpoints across KRT18 (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 PKM (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
ChiTaRS5.0N/ABC051346KRT18chr12

53343622

+PKMchr15

72499549

-


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Fusion Gene ORF analysis for KRT18-PKM

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
intron-3CDSENST00000388837ENST00000319622KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388837ENST00000565184KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388837ENST00000389093KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388837ENST00000335181KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388837ENST00000568883KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388837ENST00000449901KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388837ENST00000565154KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388837ENST00000568459KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000550600ENST00000319622KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000550600ENST00000565184KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000550600ENST00000389093KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000550600ENST00000335181KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000550600ENST00000568883KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000550600ENST00000449901KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000550600ENST00000565154KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000550600ENST00000568459KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388835ENST00000319622KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388835ENST00000565184KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388835ENST00000389093KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388835ENST00000335181KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388835ENST00000568883KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388835ENST00000449901KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388835ENST00000565154KRT18chr12

53343622

+PKMchr15

72499549

-
intron-3CDSENST00000388835ENST00000568459KRT18chr12

53343622

+PKMchr15

72499549

-

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 KRT18-PKM


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 KRT18-PKM


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
KRT18

P05783

PKM

Q99640

FUNCTION: Involved in the uptake of thrombin-antithrombin complexes by hepatic cells (By similarity). When phosphorylated, plays a role in filament reorganization. Involved in the delivery of mutated CFTR to the plasma membrane. Together with KRT8, is involved in interleukin-6 (IL-6)-mediated barrier protection. {ECO:0000250, ECO:0000269|PubMed:15529338, ECO:0000269|PubMed:16424149, ECO:0000269|PubMed:17213200, ECO:0000269|PubMed:7523419, ECO:0000269|PubMed:8522591, ECO:0000269|PubMed:9298992, ECO:0000269|PubMed:9524113}.FUNCTION: Acts as a negative regulator of entry into mitosis (G2 to M transition) by phosphorylation of the CDK1 kinase specifically when CDK1 is complexed to cyclins. Mediates phosphorylation of CDK1 predominantly on 'Thr-14'. Also involved in Golgi fragmentation. May be involved in phosphorylation of CDK1 on 'Tyr-15' to a lesser degree, however tyrosine kinase activity is unclear and may be indirect. May be a downstream target of Notch signaling pathway during eye development. {ECO:0000269|PubMed:10373560, ECO:0000269|PubMed:9001210}.

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 KRT18-PKM


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 KRT18-PKM


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 KRT18-PKM


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgenePKMQ99640DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgenePKMQ99640DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for KRT18-PKM


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKRT18C0023893Liver Cirrhosis, Experimental4CTD_human
HgeneKRT18C0006142Malignant neoplasm of breast2CTD_human
HgeneKRT18C0023903Liver neoplasms2CTD_human
HgeneKRT18C0345904Malignant neoplasm of liver2CTD_human
HgeneKRT18C0678222Breast Carcinoma2CTD_human
HgeneKRT18C1257931Mammary Neoplasms, Human2CTD_human
HgeneKRT18C1458155Mammary Neoplasms2CTD_human
HgeneKRT18C1861556Cirrhosis, Familial2CTD_human;UNIPROT
HgeneKRT18C4704874Mammary Carcinoma, Human2CTD_human
HgeneKRT18C0019193Hepatitis, Toxic1CTD_human
HgeneKRT18C0023890Liver Cirrhosis1CTD_human
HgeneKRT18C0027540Necrosis1CTD_human
HgeneKRT18C0162557Liver Failure, Acute1CTD_human
HgeneKRT18C0239946Fibrosis, Liver1CTD_human
HgeneKRT18C0860207Drug-Induced Liver Disease1CTD_human
HgeneKRT18C1262760Hepatitis, Drug-Induced1CTD_human
HgeneKRT18C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneKRT18C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneKRT18C4279912Chemically-Induced Liver Toxicity1CTD_human
TgenePKMC0027626Neoplasm Invasiveness2CTD_human
TgenePKMC0001787Osteoporosis, Age-Related1CTD_human
TgenePKMC0007097Carcinoma1CTD_human
TgenePKMC0024667Animal Mammary Neoplasms1CTD_human
TgenePKMC0024668Mammary Neoplasms, Experimental1CTD_human
TgenePKMC0029456Osteoporosis1CTD_human
TgenePKMC0029459Osteoporosis, Senile1CTD_human
TgenePKMC0205696Anaplastic carcinoma1CTD_human
TgenePKMC0205697Carcinoma, Spindle-Cell1CTD_human
TgenePKMC0205698Undifferentiated carcinoma1CTD_human
TgenePKMC0205699Carcinomatosis1CTD_human
TgenePKMC0751406Post-Traumatic Osteoporosis1CTD_human
TgenePKMC1257925Mammary Carcinoma, Animal1CTD_human
TgenePKMC2239176Liver carcinoma1CTD_human