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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 19750

FusionGeneSummary for LIN54_GDE1

check button Fusion gene summary
Fusion gene informationFusion gene name: LIN54_GDE1
Fusion gene ID: 19750
HgeneTgene
Gene symbol

LIN54

GDE1

Gene ID

132660

51573

Gene namelin-54 DREAM MuvB core complex componentglycerophosphodiester phosphodiesterase 1
SynonymsCXCDC1|JC8.6|MIP120|TCX1363E6.2|MIR16
Cytomap

4q21.22

16p12.3

Type of geneprotein-codingprotein-coding
Descriptionprotein lin-54 homologCXC domain-containing protein 1lin-54 homologglycerophosphodiester phosphodiesterase 1RGS16-interacting membrane proteinmembrane interacting protein of RGS16
Modification date2018051920180519
UniProtAcc

Q6MZP7

Q9NZC3

Ensembl transtripts involved in fusion geneENST00000395282, ENST00000395283, 
ENST00000340417, ENST00000442461, 
ENST00000446851, ENST00000510557, 
ENST00000506560, ENST00000505397, 
ENST00000505905, 
ENST00000353258, 
Fusion gene scores* DoF score2 X 2 X 2=84 X 3 X 1=12
# samples 24
** MAII scorelog2(2/8*10)=1.32192809488736log2(4/12*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LIN54 [Title/Abstract] AND GDE1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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

check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1AW881269LIN54chr4

83893284

-GDE1chr16

19513902

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-3UTRENST00000395282ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-
intron-3UTRENST00000395283ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-
intron-3UTRENST00000340417ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-
intron-3UTRENST00000442461ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-
intron-3UTRENST00000446851ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-
intron-3UTRENST00000510557ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-
intron-3UTRENST00000506560ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-
intron-3UTRENST00000505397ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-
intron-3UTRENST00000505905ENST00000353258LIN54chr4

83893284

-GDE1chr16

19513902

-

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FusionProtFeatures for LIN54_GDE1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LIN54

Q6MZP7

GDE1

Q9NZC3

Component of the DREAM complex, a multiprotein complexthat can both act as a transcription activator or repressordepending on the context (PubMed:17671431, PubMed:17531812). In G0phase, the complex binds to more than 800 promoters and isrequired for repression of E2F target genes (PubMed:17671431,PubMed:17531812). In S phase, the complex selectively binds to thepromoters of G2/M genes whose products are required for mitosisand participates in their cell cycle dependent activation(PubMed:17671431, PubMed:17531812). In the complex, acts as a DNA-binding protein that binds the promoter of CDK1 in a sequence-specific manner (PubMed:19725879). Specifically recognizes theconsensus motif 5'-TTYRAA-3' in target DNA (PubMed:27465258).{ECO:0000269|PubMed:17531812, ECO:0000269|PubMed:17671431,ECO:0000269|PubMed:19725879, ECO:0000269|PubMed:27465258}. Has glycerophosphoinositol phosphodiesterase activity.Hydrolyzes lysoglycerophospholipids to produce lysophosphatidicacid (LPA) and the corresponding amines. Has little or no activitytowards glycerophosphocholine. GDE1 activity can be modulated byG-protein signaling pathways (By similarity).{ECO:0000250|UniProtKB:Q9JL55, ECO:0000250|UniProtKB:Q9JL56}.

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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FusionGeneSequence for LIN54_GDE1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for LIN54_GDE1


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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RelatedDrugs for LIN54_GDE1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for LIN54_GDE1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneGDE1C0041696Unipolar Depression1PSYGENET
TgeneGDE1C1269683Major Depressive Disorder1PSYGENET