Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004671
Fusion event
HPV-chr18:q21.1 integration
Validated
No
Detection method
RNA-Seq
Data source
download(HPVbase)
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Normal
Reported year
2013
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Not given
Gene
E1
Start
1227
Host Sequence
Chromosome
chr18
Cytoband
q21.1
Reference genome
Start
End
45664232/48137861 (Hg38)
Location type
Intronic
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-877-3p ; hsa-mir-3147 ; hsa-mir-4689 ; hsa-mir-6858-5p ; hsa-mir-580-3p ; hsa-mir-449b-5p ; hsa-mir-449a ; hsa-mir-34c-5p ; hsa-mir-34a-5p ; hsa-mir-765 ; hsa-mir-4784 ; hsa-mir-3150b-3p ; hsa-mir-539-5p ; hsa-mir-7843-5p ; hsa-mir-6879-5p ; hsa-mir-6735-5p ; hsa-mir-4632-5p ; hsa-mir-4436b-3p ; hsa-mir-708-5p ; hsa-mir-3139 ; hsa-mir-28-5p ; hsa-mir-106b-3p ; hsa-mir-1228-3p ; hsa-mir-8485 ; hsa-mir-4650-5p ; hsa-mir-1972 ; hsa-mir-510-5p ; hsa-mir-1976 ; hsa-mir-6894-3p ; hsa-mir-4290 ; hsa-mir-18a-3p ; hsa-mir-5193 ; hsa-mir-4667-3p
Nearest miRNA
hsa-mir-1-2/Upstream/757296; hsa-mir-122/Downstream/532739;
Nearest CpG islands
None/Target, chr18-CpG: 67/Upstream/712, chr18-CpG: 58/Downstream/23565
Nearest cancer related gene
ZBTB7C(TSG, No orient, 0)
Upstream sequence
GGTGTGGCCAAACACCCTCTCCCAGGCCTTTCCTTCAAACCTCACACAAACCTCTCCTTCGAGCCTTCTTGAAAACTGCCACCTGGGAGGCTCTGGCCAG
Downstream sequence
AACACCCTCTCCCAGGCCTTTCCTTCAAACCTCACACAAACCTCTCCTTCGAGCCTTCTTGAAAACTGCCACCTGGGAGGCTCTGGCCAGCTGGGTGCTG
Reference
Khoury, J. D., et al. Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq. J Virol,2013, 87(16): 8916-8926.