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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:HCP5-YBX1 (FusionGDB2 ID:HG10866TG4904)

Fusion Gene Summary for HCP5-YBX1

check button Fusion gene summary
Fusion gene informationFusion gene name: HCP5-YBX1
Fusion gene ID: hg10866tg4904
HgeneTgene
Gene symbol

HCP5

YBX1

Gene ID

10866

4904

Gene nameHLA complex P5Y-box binding protein 1
Synonyms6S2650E|D6S2650E|P5-1BP-8|CBF-A|CSDA2|CSDB|DBPB|EFI-A|MDR-NF1|NSEP-1|NSEP1|YB-1|YB1
Cytomap('HCP5')('YBX1')

6p21.33

1p34.2

Type of genencRNAprotein-coding
DescriptionHLA class I histocompatibility antigen protein P5HLA complex P5 (non-protein coding)HLA complex protein P5MHC class I region ORFY-box-binding protein 1CCAAT-binding transcription factor I subunit ADNA-binding protein BY-box transcription factorenhancer factor I subunit Amajor histocompatibility complex, class II, Y box-binding protein Inuclease-sensitive element-binding prot
Modification date2020031320200327
UniProtAcc

Q6MZN7

.
Ensembl transtripts involved in fusion geneENST00000414046, ENST00000419355, 
ENST00000423496, ENST00000457127, 
Fusion gene scores* DoF score8 X 5 X 6=2408 X 7 X 6=336
# samples 98
** MAII scorelog2(9/240*10)=-1.41503749927884
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/336*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HCP5 [Title/Abstract] AND YBX1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHCP5(31368540)-YBX1(43166452), # 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
TgeneYBX1

GO:0006355

regulation of transcription, DNA-templated

18809583

TgeneYBX1

GO:0045944

positive regulation of transcription by RNA polymerase II

18809583

TgeneYBX1

GO:0048255

mRNA stabilization

31358969

TgeneYBX1

GO:1990428

miRNA transport

27559612



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
ChimerDB4STADTCGA-BR-8366-01AHCP5chr6

31368540

+YBX1chr1

43166452

+


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Fusion Gene ORF analysis for HCP5-YBX1

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
3UTR-3CDSENST00000414046ENST00000321358HCP5chr6

31368540

+YBX1chr1

43166452

+
3UTR-intronENST00000414046ENST00000467957HCP5chr6

31368540

+YBX1chr1

43166452

+
intron-3CDSENST00000419355ENST00000321358HCP5chr6

31368540

+YBX1chr1

43166452

+
intron-3CDSENST00000423496ENST00000321358HCP5chr6

31368540

+YBX1chr1

43166452

+
intron-3CDSENST00000457127ENST00000321358HCP5chr6

31368540

+YBX1chr1

43166452

+
intron-intronENST00000419355ENST00000467957HCP5chr6

31368540

+YBX1chr1

43166452

+
intron-intronENST00000423496ENST00000467957HCP5chr6

31368540

+YBX1chr1

43166452

+
intron-intronENST00000457127ENST00000467957HCP5chr6

31368540

+YBX1chr1

43166452

+

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 HCP5-YBX1


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)
HCP5chr631368540+YBX1chr143166451+4.12E-060.9999958
HCP5chr631368540+YBX1chr143166451+4.12E-060.9999958


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 HCP5-YBX1


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/:31368540/:43166452)
- 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
HCP5

Q6MZN7

.
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


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Fusion Gene Sequence for HCP5-YBX1


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 HCP5-YBX1


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 HCP5-YBX1


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 HCP5-YBX1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007102Malignant tumor of colon1CTD_human
TgeneC0009375Colonic Neoplasms1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0027643Neoplasm Recurrence, Local1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human