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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:CHI3L1-GMDS (FusionGDB2 ID:HG1116TG2762)

Fusion Gene Summary for CHI3L1-GMDS

check button Fusion gene summary
Fusion gene informationFusion gene name: CHI3L1-GMDS
Fusion gene ID: hg1116tg2762
HgeneTgene
Gene symbol

CHI3L1

GMDS

Gene ID

1116

2762

Gene namechitinase 3 like 1GDP-mannose 4,6-dehydratase
SynonymsASRT7|CGP-39|GP-39|GP39|HC-gp39|HCGP-3P|YK-40|YKL-40|YKL40|YYL-40|hCGP-39GMD|SDR3E1
Cytomap('CHI3L1')('GMDS')

1q32.1

6p25.3

Type of geneprotein-codingprotein-coding
Descriptionchitinase-3-like protein 139 kDa synovial proteincartilage glycoprotein 39chitinase 3-like 1 (cartilage glycoprotein-39)GDP-mannose 4,6 dehydrataseGDP-D-mannose dehydrataseshort chain dehydrogenase/reductase family 3E, member 1
Modification date2020031320200313
UniProtAcc

P36222

O60547

Ensembl transtripts involved in fusion geneENST00000255409, 
Fusion gene scores* DoF score13 X 8 X 7=72814 X 10 X 8=1120
# samples 1315
** MAII scorelog2(13/728*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(15/1120*10)=-2.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHI3L1 [Title/Abstract] AND GMDS [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHI3L1(203148064)-GMDS(2235871), # 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
TgeneGMDS

GO:0019673

GDP-mannose metabolic process

9525924

TgeneGMDS

GO:0042351

'de novo' GDP-L-fucose biosynthetic process

9525924



check button Fusion gene information
* 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


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Fusion Gene ORF analysis for CHI3L1-GMDS

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

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 CHI3L1-GMDS


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)


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Fusion Protein Features for CHI3L1-GMDS


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/:203148064/:2235871)
- 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
CHI3L1

P36222

GMDS

O60547

FUNCTION: Carbohydrate-binding lectin with a preference for chitin. Has no chitinase activity. May play a role in tissue remodeling and in the capacity of cells to respond to and cope with changes in their environment. Plays a role in T-helper cell type 2 (Th2) inflammatory response and IL-13-induced inflammation, regulating allergen sensitization, inflammatory cell apoptosis, dendritic cell accumulation and M2 macrophage differentiation. Facilitates invasion of pathogenic enteric bacteria into colonic mucosa and lymphoid organs. Mediates activation of AKT1 signaling pathway and subsequent IL8 production in colonic epithelial cells. Regulates antibacterial responses in lung by contributing to macrophage bacterial killing, controlling bacterial dissemination and augmenting host tolerance. Also regulates hyperoxia-induced injury, inflammation and epithelial apoptosis in lung. {ECO:0000269|PubMed:16472595, ECO:0000269|PubMed:19414556, ECO:0000269|PubMed:20558631, ECO:0000269|PubMed:9492324}.FUNCTION: Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose. {ECO:0000269|PubMed:9525924}.

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 CHI3L1-GMDS


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 CHI3L1-GMDS


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 CHI3L1-GMDS


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 CHI3L1-GMDS


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCHI3L1C0017636Glioblastoma1CTD_human
HgeneCHI3L1C0017638Glioma1CTD_human
HgeneCHI3L1C0027626Neoplasm Invasiveness1CTD_human
HgeneCHI3L1C0029408Degenerative polyarthritis1CTD_human
HgeneCHI3L1C0086743Osteoarthrosis Deformans1CTD_human
HgeneCHI3L1C0259783mixed gliomas1CTD_human
HgeneCHI3L1C0334588Giant Cell Glioblastoma1CTD_human
HgeneCHI3L1C0555198Malignant Glioma1CTD_human
HgeneCHI3L1C1621958Glioblastoma Multiforme1CTD_human