Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003727
Fusion event
HPV-chr13 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Perfect
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Start
177
End
110
Orient
-
Integrated sequence
AGGACCCACAGGAGCGACCCAGAAAGTTACCACAGTTATGCACAGAGCTGCAAACAACTATACATGAT
Host Sequence
Chromosome
chr13
Cytoband
q22.1
Reference genome
Start
End
73788866/73214729 (Hg38)
Location type
Intronic
Fragile sites / regions
miRNAs that regulate target gene
hsa-mir-145-5p ; hsa-mir-141-3p ; hsa-mir-9-5p ; hsa-mir-128-3p ; hsa-mir-101-3p ; hsa-mir-21-5p ; hsa-mir-23a-3p ; hsa-mir-143-3p ; hsa-mir-4652-3p ; hsa-mir-4743-3p ; hsa-mir-218-5p ; hsa-mir-4480 ; hsa-mir-489-3p ; hsa-mir-4668-3p ; hsa-mir-4679 ; hsa-mir-4677-3p ; hsa-mir-216b-5p ; hsa-mir-1264 ; hsa-mir-6888-3p ; hsa-mir-4775 ; hsa-mir-215-3p ; hsa-mir-6773-3p ; hsa-mir-34a-5p ; hsa-mir-141-3p ; hsa-mir-137 ; hsa-mir-153-3p ; hsa-mir-200a-3p ; hsa-mir-4720-3p ; hsa-mir-4804-3p
Nearest miRNA
hsa-mir-1297/Upstream/6996405; hsa-mir-1267/Downstream/4483283;
Nearest CpG islands
Nearest cancer related gene
KLF5(TSG, No orient, 0)
Downstream sequence
AATACAAAAATTAGCTGGGTGTAGTGGCACACGCCTGTAATCCCAGCTACTCGGGAGGCTGGGGAAGGAGAATCACTTGAACCTGGGAGG
Junction sequence
AGGCGACGGCTTTGGTATGGGTCGCGGCGGAGTGGTTGGCCAAGTGCTGCCTAATACAAAAATTAGCTGGGTGTAGTGGCACACGCCTGTAATCCCAGCTACTCGGGAGGCTGGGGAAGGAGAATCACTTGAACCTGGGAGG
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
Reference
Liu, Y., et al. Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology. Oncotarget,2016, 7(5): 5852-5864.