Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003908
Fusion event
HPV-ERBB2 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Not given
Gene
E1
Start
5626
Host Sequence
Chromosome
chr17
Cytoband
q12
Reference genome
Start
End
37850836/39694583 (Hg38)
Location type
Intron3
Target gene
miRNAs that regulate target gene
hsa-mir-559 ; hsa-mir-548d-3p ; hsa-mir-125b-5p ; hsa-mir-21-5p ; hsa-mir-125a-5p ; hsa-mir-331-3p ; hsa-mir-205-5p ; hsa-mir-199b-5p ; hsa-mir-199a-5p ; hsa-mir-124-3p ; hsa-mir-326 ; hsa-mir-375 ; hsa-mir-25-3p ; hsa-mir-670-3p ; hsa-mir-4326 ; hsa-mir-552-3p ; hsa-mir-541-3p ; hsa-mir-498 ; hsa-mir-323b-5p ; hsa-mir-193a-5p ; hsa-mir-193a-3p ; hsa-mir-134-5p ; hsa-mir-6739-3p ; hsa-mir-4677-5p ; hsa-mir-7156-5p ; hsa-mir-4273 ; hsa-mir-7109-5p ; hsa-mir-4790-5p ; hsa-mir-6868-3p ; hsa-mir-3127-5p ; hsa-mir-22-5p ; hsa-mir-2116-5p ; hsa-mir-593-3p ; hsa-mir-6885-5p ; hsa-mir-328-5p ; hsa-mir-6887-5p ; hsa-mir-486-3p ; hsa-mir-6795-5p ; hsa-mir-3140-3p ; hsa-mir-3116 ; hsa-mir-1254 ; hsa-mir-4790-3p ; hsa-mir-6730-3p ; hsa-mir-4680-3p ; hsa-mir-5187-3p ; hsa-mir-4427 ; hsa-mir-4653-5p ; hsa-mir-3921 ; hsa-mir-301b-5p ; hsa-mir-301a-5p ; hsa-mir-4315 ; hsa-mir-146a-3p ; hsa-mir-3667-3p ; hsa-mir-6734-3p ; hsa-mir-6891-3p ; hsa-mir-6072 ; hsa-mir-6754-5p ; hsa-mir-4441 ; hsa-mir-4270 ; hsa-mir-211-3p ; hsa-mir-4748 ; hsa-mir-329-5p ; hsa-mir-4464 ; hsa-mir-7845-5p ; hsa-mir-888-3p ; hsa-mir-4506 ; hsa-mir-34a-5p ; hsa-mir-155-3p ; hsa-mir-130b-3p ; hsa-mir-1296-5p ; hsa-mir-133a-3p ; hsa-mir-3622b-5p ; hsa-mir-22-3p
Nearest miRNA
hsa-mir-1180/Upstream/397074; hsa-mir-10226/Downstream/31912;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/6355, chr17-CpG: 56/Downstream/5517
Nearest cancer related gene
ERBB2(OG, No orient, 0)
Upstream sequence
AAACACCAAAGTGTCTAAACAATTACAATAGGTAATAGAAAGCTACTAGTGAGGCCAAGGCCTCACATTTCTTAATTATTTTCTTTTTTTCTCCACAGTA
Downstream sequence
gaatcaaCCAGGTGGGTTCAGTGAATGAAACCATCAGAAACGAATTGTCCCCTGAAATCAAGACTTTGTGATTGCCATAGTTGTATGCTTCTCAAAGGTT
Reference
Koneva, L. A., et al. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res ,2018,16(1): 90-102.