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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:LIMS1-CCDC138 (FusionGDB2 ID:44731)

Fusion Gene Summary for LIMS1-CCDC138

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMS1-CCDC138
Fusion gene ID: 44731
HgeneTgene
Gene symbol

LIMS1

CCDC138

Gene ID

3987

165055

Gene nameLIM zinc finger domain containing 1coiled-coil domain containing 138
SynonymsPINCH|PINCH-1|PINCH1-
Cytomap

2q12.3

2q13

Type of geneprotein-codingprotein-coding
DescriptionLIM and senescent cell antigen-like-containing domain protein 1LIM and senescent cell antigen-like domains 1LIM-type zinc finger domains 1particularly interesting new Cys-His protein 1renal carcinoma antigen NY-REN-48senescent cell antigencoiled-coil domain-containing protein 138
Modification date2020032720200313
UniProtAcc

P48059

Q96M89

Ensembl transtripts involved in fusion geneENST00000544547, ENST00000332345, 
ENST00000338045, ENST00000393310, 
ENST00000393314, ENST00000409441, 
ENST00000410093, ENST00000462817, 
ENST00000542845, 		ENST00000470608, 
ENST00000295124, ENST00000412964, 
Fusion gene scores* DoF score9 X 4 X 6=2164 X 4 X 3=48
# samples 84
** MAII scorelog2(8/216*10)=-1.43295940727611
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: LIMS1 [Title/Abstract] AND CCDC138 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIMS1(109151050)-CCDC138(109421345), # 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneLIMS1

GO:0045892

negative regulation of transcription, DNA-templated

21390327


check buttonFusion gene breakpoints across LIMS1 (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 CCDC138 (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
ChimerDB4BLCATCGA-K4-A5RJ-01ALIMS1chr2

109151050

+CCDC138chr2

109421345

+


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Fusion Gene ORF analysis for LIMS1-CCDC138

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
5CDS-intronENST00000544547ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
Frame-shiftENST00000544547ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
Frame-shiftENST00000544547ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000332345ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000332345ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000338045ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000338045ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000393310ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000393310ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000393314ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000393314ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000409441ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000409441ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000410093ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000410093ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000462817ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000462817ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000542845ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000542845ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000332345ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000338045ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000393310ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000393314ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000409441ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000410093ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000462817ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000542845ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+

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 LIMS1-CCDC138


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)
LIMS1chr2109151050+CCDC138chr2109421344+2.21E-121
LIMS1chr2109151050+CCDC138chr2109421344+2.21E-121

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.
genomic feature of top 1%

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Fusion Protein Features for LIMS1-CCDC138


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:109151050/:109421345)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LIMS1

P48059

CCDC138

Q96M89

FUNCTION: Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Involved in the regulation of cell survival, cell proliferation and cell differentiation.

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 LIMS1-CCDC138


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 LIMS1-CCDC138


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 LIMS1-CCDC138


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 LIMS1-CCDC138


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource