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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: 14527

FusionGeneSummary for GDE1_COL9A3

check button Fusion gene summary
Fusion gene informationFusion gene name: GDE1_COL9A3
Fusion gene ID: 14527
HgeneTgene
Gene symbol

GDE1

COL9A3

Gene ID

51573

1299

Gene nameglycerophosphodiester phosphodiesterase 1collagen type IX alpha 3 chain
Synonyms363E6.2|MIR16DJ885L7.4.1|EDM3|IDD|MED
Cytomap

16p12.3

20q13.33

Type of geneprotein-codingprotein-coding
Descriptionglycerophosphodiester phosphodiesterase 1RGS16-interacting membrane proteinmembrane interacting protein of RGS16collagen alpha-3(IX) chaincollagen IX, alpha-3 polypeptidecollagen type IX proteoglycancollagen, type IX, alpha 3
Modification date2018051920180523
UniProtAcc

Q9NZC3

Q14050

Ensembl transtripts involved in fusion geneENST00000353258, ENST00000343916, 
ENST00000462700, 
Fusion gene scores* DoF score5 X 5 X 3=752 X 2 X 2=8
# samples 52
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: GDE1 [Title/Abstract] AND COL9A3 [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
ChiTaRS3.1DA571660GDE1chr16

19533250

-COL9A3chr20

61461913

+
* 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-3CDSENST00000353258ENST00000343916GDE1chr16

19533250

-COL9A3chr20

61461913

+
intron-intronENST00000353258ENST00000462700GDE1chr16

19533250

-COL9A3chr20

61461913

+

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FusionProtFeatures for GDE1_COL9A3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
GDE1

Q9NZC3

COL9A3

Q14050

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}. Structural component of hyaline cartilage and vitreousof the eye.

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 GDE1_COL9A3


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 GDE1_COL9A3


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 GDE1_COL9A3


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 GDE1_COL9A3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGDE1C0041696Unipolar Depression1PSYGENET
HgeneGDE1C1269683Major Depressive Disorder1PSYGENET
TgeneCOL9A3C1832998EPIPHYSEAL DYSPLASIA, MULTIPLE, 31CTD_human;UNIPROT