hsa-mir-885-3p _HNSC.png
hsa-mir-338-5p _HNSC.png
CD274 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004266
Fusion event
HPV-CD274 integration
Validated
Yes
Detection method
WGS, RNA-seq, Whole-Exome sequencing, PCR
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
25313082
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
AY686584
Region type
LCR
Start
7848
Integrated sequence
ATAAGGTTTAAACTTCTAAGGCCAACTAAATGTCACCCTAGTTCATACATGAACTGTGTAAAGGTTAGTCATACATTGTTCATTTGTAAAACTGCACATG| |GGTGTGTGCAAACCGTTTTGGGTTACACATTTACAAGCAACTTATATAATAATACTAA
Host Sequence
Chromosome
chr9
Cytoband
p24.1
Reference genome
GRCh37/hg19
Start
5464244/5464244 (Hg38)
End
5464244/5464244 (Hg38)
Location type
Intronic
Target gene
CD274
miRNAs that regulate target gene
hsa-mir-513a-5p ; hsa-mir-103a-3p ; hsa-mir-16-5p ; hsa-mir-570-3p ; hsa-mir-651-3p ; hsa-mir-3978 ; hsa-mir-593-3p ; hsa-mir-885-3p ; hsa-mir-380-5p ; hsa-mir-124-3p ; hsa-mir-601 ; hsa-mir-708-5p ; hsa-mir-34b-5p ; hsa-mir-665 ; hsa-mir-940 ; hsa-mir-326 ; hsa-mir-363-5p ; hsa-mir-214-3p ; hsa-mir-29c-3p ; hsa-mir-3977 ; hsa-mir-5706 ; hsa-mir-4782-5p ; hsa-mir-516b-5p ; hsa-mir-1299 ; hsa-mir-103a-2-5p ; hsa-mir-4790-3p ; hsa-mir-6128 ; hsa-mir-875-3p ; hsa-mir-4496 ; hsa-mir-138-5p ; hsa-mir-324-5p ; hsa-mir-338-5p ; hsa-mir-34a-3p ; hsa-mir-152-5p ; hsa-mir-200b-3p ; hsa-mir-152-3p ; hsa-mir-1273a ; hsa-mir-1273c ; hsa-mir-15a-5p ; hsa-mir-15b-5p ; hsa-mir-194-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-4503 ; hsa-mir-497-5p ; hsa-mir-6792-5p ; hsa-mir-6838-5p
Nearest miRNA
hsa-mir-101-2/Upstream/613869; hsa-let-7a-1/Downstream/543582;
Nearest TSS
ENST00000422679/Upstream/1309; ENST00000397747/Downstream/46326;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/13615, chr9-CpG: 107/Downstream/164326
Junction sequence
TTGAACTGGCTTTCAGTAAAAGCTAGATTAGTGGGTTCCTGCCATTTACAAGCTGTTTTATGACA---ACCCATGTGCAGTTTTACAAATGAACAATGTATGAC
* 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.
Curate