Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CD74-CD40 (FusionGDB2 ID:HG972TG958)

Fusion Gene Summary for CD74-CD40

check button Fusion gene summary
Fusion gene informationFusion gene name: CD74-CD40
Fusion gene ID: hg972tg958
HgeneTgene
Gene symbol

CD74

CD40

Gene ID

972

958

Gene nameCD74 moleculeCD40 molecule
SynonymsDHLAG|HLADG|II|Ia-GAMMA|p33Bp50|CDW40|TNFRSF5|p50
Cytomap('CD74')('CD40')

5q33.1

20q13.12

Type of geneprotein-codingprotein-coding
DescriptionHLA class II histocompatibility antigen gamma chainCD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)CD74 molecule, major histocompatibility complex, class II invariant chainHLA-DR antigens-associated tumor necrosis factor receptor superfamily member 5B cell surface antigen CD40B cell-associated moleculeCD40 molecule, TNF receptor superfamily member 5CD40L receptor
Modification date2020031320200327
UniProtAcc

P04233

.
Ensembl transtripts involved in fusion geneENST00000377795, ENST00000009530, 
ENST00000353334, ENST00000524315, 
Fusion gene scores* DoF score43 X 51 X 20=438606 X 4 X 4=96
# samples 596
** MAII scorelog2(59/43860*10)=-6.21604704731175
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/96*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CD74 [Title/Abstract] AND CD40 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCD74(149781200)-CD40(44754189), # 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
HgeneCD74

GO:0001516

prostaglandin biosynthetic process

12782713

HgeneCD74

GO:0001934

positive regulation of protein phosphorylation

24942581

HgeneCD74

GO:0002792

negative regulation of peptide secretion

19849849

HgeneCD74

GO:0033674

positive regulation of kinase activity

24942581

HgeneCD74

GO:0043066

negative regulation of apoptotic process

12782713

HgeneCD74

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

24942581

HgeneCD74

GO:0043410

positive regulation of MAPK cascade

24942581

HgeneCD74

GO:0043518

negative regulation of DNA damage response, signal transduction by p53 class mediator

17045821

HgeneCD74

GO:0045657

positive regulation of monocyte differentiation

24942581

HgeneCD74

GO:0045893

positive regulation of transcription, DNA-templated

24942581

HgeneCD74

GO:0046598

positive regulation of viral entry into host cell

24942581

HgeneCD74

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

17045821

HgeneCD74

GO:0070374

positive regulation of ERK1 and ERK2 cascade

17045821|24942581

TgeneCD40

GO:0023035

CD40 signaling pathway

31331973

TgeneCD40

GO:2000353

positive regulation of endothelial cell apoptotic process

12885753



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
ChimerDB4BLCATCGA-XF-A9T5-01ACD74chr5

149781200

-CD40chr20

44754189

+


Top

Fusion Gene ORF analysis for CD74-CD40

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-intronENST00000377795ENST00000372276CD74chr5

149781200

-CD40chr20

44754189

+
5CDS-intronENST00000377795ENST00000372285CD74chr5

149781200

-CD40chr20

44754189

+
5CDS-intronENST00000377795ENST00000489304CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000009530ENST00000372276CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000009530ENST00000372285CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000009530ENST00000489304CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000353334ENST00000372276CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000353334ENST00000372285CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000353334ENST00000489304CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000524315ENST00000372276CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000524315ENST00000372285CD74chr5

149781200

-CD40chr20

44754189

+
intron-intronENST00000524315ENST00000489304CD74chr5

149781200

-CD40chr20

44754189

+

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

Top

Fusion Genomic Features for CD74-CD40


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)


Top

Fusion Protein Features for CD74-CD40


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/:149781200/:44754189)
- 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
CD74

P04233

.
FUNCTION: Plays a critical role in MHC class II antigen processing by stabilizing peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to the endosomal/lysosomal system where the antigen processing and binding of antigenic peptides to MHC class II takes place. Serves as cell surface receptor for the cytokine MIF.; FUNCTION: [Class-II-associated invariant chain peptide]: Binds to the peptide-binding site of MHC class II alpha/beta heterodimers forming an alpha-beta-CLIP complex, thereby preventing the loading of antigenic peptides to the MHC class II complex until its release by HLA-DM in the endosome. {ECO:0000269|PubMed:1448172}.; FUNCTION: [Isoform p41]: Stabilizes the conformation of mature CTSL by binding to its active site and serving as a chaperone to help maintain a pool of mature enzyme in endocytic compartments and extracellular space of antigen-presenting cells (APCs). Has antiviral activity by stymieing the endosomal entry of Ebola virus and coronaviruses, including SARS-CoV-2 (PubMed:32855215). Disrupts cathepsin-mediated Ebola virus glycoprotein processing, which prevents viral fusion and entry. This antiviral activity is specific to p41 isoform (PubMed:32855215). {ECO:0000250|UniProtKB:P04441, ECO:0000269|PubMed:32855215}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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


Top

Fusion Gene Sequence for CD74-CD40


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.

Top

Fusion Gene PPI Analysis for CD74-CD40


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


Top

Related Drugs for CD74-CD40


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for CD74-CD40


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCD74C0006142Malignant neoplasm of breast1CTD_human
HgeneCD74C0007131Non-Small Cell Lung Carcinoma1CTD_human
HgeneCD74C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCD74C0162557Liver Failure, Acute1CTD_human
HgeneCD74C0678222Breast Carcinoma1CTD_human
HgeneCD74C1257931Mammary Neoplasms, Human1CTD_human
HgeneCD74C1458155Mammary Neoplasms1CTD_human
HgeneCD74C4704874Mammary Carcinoma, Human1CTD_human
TgeneC0003873Rheumatoid Arthritis3CTD_human
TgeneC1720957Hyper-IgM Immunodeficiency Syndrome, Type 33CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0026691Mucocutaneous Lymph Node Syndrome2CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0020456Hyperglycemia1CTD_human
TgeneC0020459Hyperinsulinism1CTD_human
TgeneC0021655Insulin Resistance1CTD_human
TgeneC0026769Multiple Sclerosis1CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0038220Status Epilepticus1CTD_human
TgeneC0270823Petit mal status1CTD_human
TgeneC0311335Grand Mal Status Epilepticus1CTD_human
TgeneC0393734Complex Partial Status Epilepticus1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0751324Multiple Sclerosis, Acute Fulminating1CTD_human
TgeneC0751522Status Epilepticus, Subclinical1CTD_human
TgeneC0751523Non-Convulsive Status Epilepticus1CTD_human
TgeneC0751524Simple Partial Status Epilepticus1CTD_human
TgeneC0920563Insulin Sensitivity1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1257963Endogenous Hyperinsulinism1CTD_human
TgeneC1257964Exogenous Hyperinsulinism1CTD_human
TgeneC1257965Compensatory Hyperinsulinemia1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1855520Hyperglycemia, Postprandial1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human