Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20005047
Fusion event
HPV-DNAJC15 integration
Validated
No
Detection method
WGS, RNA-seq, Whole-Exome sequencing, PCR
Data source
Curated
Sample type
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV33
Reference genome
Not given
Gene
E1
Start
2460
Host Sequence
Chromosome
chr13
Cytoband
q14.11
Reference genome
Start
End
43679085/43104949 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-8068 ; hsa-mir-5087 ; hsa-mir-657 ; hsa-mir-3665 ; hsa-mir-4748 ; hsa-mir-4464 ; hsa-mir-5580-3p ; hsa-mir-5589-3p ; hsa-mir-574-5p ; hsa-mir-135b-3p ; hsa-mir-4278 ; hsa-mir-6867-5p ; hsa-mir-6887-5p ; hsa-mir-6795-5p ; hsa-mir-625-5p ; hsa-mir-6732-5p ; hsa-mir-6805-5p ; hsa-mir-6794-5p ; hsa-mir-4716-3p ; hsa-mir-129-5p ; hsa-mir-3680-3p ; hsa-mir-557 ; hsa-mir-507 ; hsa-mir-450b-5p
Nearest miRNA
hsa-mir-2276/Upstream/1536554; hsa-mir-1267/Downstream/1091180;
Nearest CpG islands
Junction sequence
CTGGTCTCAGACTCCTGGGCTCAAGTGATCCTCTCACCTCACCCTCCCA---AAGCATCTATATATGTCCAACTTATTGGCGTTACATCATCTATCATTCCTAT
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
Reference
Parfenov, M., et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A,2014,111(43): 15544-15549.