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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:LDB2-PKD2 (FusionGDB2 ID:44066)

Fusion Gene Summary for LDB2-PKD2

check button Fusion gene summary
Fusion gene informationFusion gene name: LDB2-PKD2
Fusion gene ID: 44066
HgeneTgene
Gene symbol

LDB2

PKD2

Gene ID

9079

25865

Gene nameLIM domain binding 2protein kinase D2
SynonymsCLIM1|LDB-2|LDB1HSPC187|PKD2|nPKC-D2
Cytomap

4p15.32

19q13.32

Type of geneprotein-codingprotein-coding
DescriptionLIM domain-binding protein 2LIM binding domain 2LIM domain-binding factor CLIM1LIM domain-binding factor-2carboxyl-terminal LIM domain-binding protein 1serine/threonine-protein kinase D2
Modification date2020031320200329
UniProtAcc

O43679

.
Ensembl transtripts involved in fusion geneENST00000515064, ENST00000441778, 
ENST00000304523, ENST00000502640, 
ENST00000503178, ENST00000503829, 
ENST00000237596, ENST00000508588, 
ENST00000511337, ENST00000502363, 
Fusion gene scores* DoF score6 X 6 X 2=724 X 4 X 3=48
# samples 64
** MAII scorelog2(6/72*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LDB2 [Title/Abstract] AND PKD2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLDB2(16899977)-PKD2(88940610), # samples:1
Anticipated loss of major functional domain due to fusion event.LDB2-PKD2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
LDB2-PKD2 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* 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
TgenePKD2

GO:0006468

protein phosphorylation

22228765

TgenePKD2

GO:0018105

peptidyl-serine phosphorylation

18440775

TgenePKD2

GO:0045944

positive regulation of transcription by RNA polymerase II

17077180

TgenePKD2

GO:0046777

protein autophosphorylation

17077180

TgenePKD2

GO:0050852

T cell receptor signaling pathway

17077180


check buttonFusion gene breakpoints across LDB2 (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 PKD2 (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-BR-8365-01ALDB2chr4

16899977

-PKD2chr4

88940610

+


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Fusion Gene ORF analysis for LDB2-PKD2

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
Frame-shiftENST00000515064ENST00000237596LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000515064ENST00000508588LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000515064ENST00000511337LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000515064ENST00000502363LDB2chr4

16899977

-PKD2chr4

88940610

+
Frame-shiftENST00000441778ENST00000237596LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000441778ENST00000508588LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000441778ENST00000511337LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000441778ENST00000502363LDB2chr4

16899977

-PKD2chr4

88940610

+
Frame-shiftENST00000304523ENST00000237596LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000304523ENST00000508588LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000304523ENST00000511337LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000304523ENST00000502363LDB2chr4

16899977

-PKD2chr4

88940610

+
Frame-shiftENST00000502640ENST00000237596LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000502640ENST00000508588LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000502640ENST00000511337LDB2chr4

16899977

-PKD2chr4

88940610

+
5CDS-intronENST00000502640ENST00000502363LDB2chr4

16899977

-PKD2chr4

88940610

+
intron-3CDSENST00000503178ENST00000237596LDB2chr4

16899977

-PKD2chr4

88940610

+
intron-intronENST00000503178ENST00000508588LDB2chr4

16899977

-PKD2chr4

88940610

+
intron-intronENST00000503178ENST00000511337LDB2chr4

16899977

-PKD2chr4

88940610

+
intron-intronENST00000503178ENST00000502363LDB2chr4

16899977

-PKD2chr4

88940610

+
intron-3CDSENST00000503829ENST00000237596LDB2chr4

16899977

-PKD2chr4

88940610

+
intron-intronENST00000503829ENST00000508588LDB2chr4

16899977

-PKD2chr4

88940610

+
intron-intronENST00000503829ENST00000511337LDB2chr4

16899977

-PKD2chr4

88940610

+
intron-intronENST00000503829ENST00000502363LDB2chr4

16899977

-PKD2chr4

88940610

+

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 LDB2-PKD2


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)
LDB2chr416899976-PKD2chr488940609+2.07E-070.99999976
LDB2chr416899976-PKD2chr488940609+2.07E-070.99999976

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 LDB2-PKD2


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
LDB2

O43679

.
FUNCTION: Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors.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.

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 LDB2-PKD2


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 LDB2-PKD2


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 LDB2-PKD2


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 LDB2-PKD2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgenePKD2C2751306Polycystic kidney disease, type 223CTD_human;GENOMICS_ENGLAND;UNIPROT
TgenePKD2C0085413Polycystic Kidney, Autosomal Dominant20CLINGEN;CTD_human;GENOMICS_ENGLAND
TgenePKD2C0022680Polycystic Kidney Diseases12CLINGEN
TgenePKD2C0887850Polycystic Kidney, Type 1 Autosomal Dominant Disease6CTD_human
TgenePKD2C0023893Liver Cirrhosis, Experimental1CTD_human
TgenePKD2C0035309Retinal Diseases1CTD_human
TgenePKD2C0042373Vascular Diseases1CTD_human
TgenePKD2C0270715Degenerative Diseases, Central Nervous System1CTD_human
TgenePKD2C0524851Neurodegenerative Disorders1CTD_human
TgenePKD2C0751733Degenerative Diseases, Spinal Cord1CTD_human