Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004545
Fusion event
HPV-PDK3 integration
Validated
Yes
Detection method
Multiplex RT-PCR, APOT assay
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Normal
Reported year
2014
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Gene
E2
Start
1703
Integrated sequence
CATTTGGACTTACACCCAGTATAGCTGAC AGTATAAAAACACTATTACAACAATATTGTTTATATTTACACATTCAAAGTTTAGCATGTTCATGGGGAA| | TGGTTGTGTTACTATTAGTAAGATATAAATGTGGAAAAAATAGAGAAACAATTGAAAAATTGCTGTCTAA ACTATTATGTGTGTCTCCAATGTGTATG
Host Sequence
Chromosome
chrX
Cytoband
p22.11
Reference genome
Start
End
24564835/24546718 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-655-3p ; hsa-mir-374c-5p ; hsa-mir-6765-3p ; hsa-mir-3622b-3p ; hsa-mir-3622a-3p ; hsa-mir-369-3p ; hsa-mir-892c-3p ; hsa-mir-4676-3p ; hsa-mir-452-5p ; hsa-mir-1273e ; hsa-mir-377-3p ; hsa-mir-3200-3p ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-6516-5p ; hsa-mir-455-3p ; hsa-mir-7703 ; hsa-mir-6720-5p ; hsa-mir-6512-3p ; hsa-mir-1227-3p ; hsa-mir-658 ; hsa-mir-4252 ; hsa-mir-6499-3p ; hsa-mir-6086 ; hsa-mir-377-5p ; hsa-mir-4537 ; hsa-mir-1273f ; hsa-mir-4793-3p ; hsa-mir-766-3p ; hsa-mir-1273g-3p ; hsa-mir-508-5p ; hsa-mir-6818-3p ; hsa-mir-4684-5p ; hsa-mir-593-3p ; hsa-mir-6895-3p ; hsa-mir-196a-3p ; hsa-mir-5699-3p ; hsa-mir-4421 ; hsa-mir-339-5p ; hsa-mir-10b-5p ; hsa-mir-10a-5p ; hsa-mir-6732-3p ; hsa-mir-5007-3p ; hsa-mir-3160-5p ; hsa-mir-4262 ; hsa-mir-181d-5p ; hsa-mir-181c-5p ; hsa-mir-181b-5p ; hsa-mir-181a-5p ; hsa-mir-3190-5p ; hsa-mir-340-3p ; hsa-mir-3613-3p ; hsa-mir-3926 ; hsa-mir-4786-5p ; hsa-mir-548s ; hsa-mir-6771-3p ; hsa-mir-6827-3p ; hsa-mir-6849-3p
Nearest miRNA
hsa-mir-23c/Upstream/4529531; hsa-let-7f-2/Downstream/3948837;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/80888, chrX-CpG: 56/Downstream/146795
Upstream sequence
tgaatagtaaaacaaccctgtacatcatccagcttcaacaattatcaatATGCTGTCATTTATGAGTCGCCTATATGCCTAGACATTCCCATTATTTTTT
Downstream sequence
GGGGGTAGAGCTGAGTGACCCAGCAGTGGGAGATTTAACAACTGGAGAAGAAGATGGGATGTGTTTAATTATCCCCAGAGGTAGGGCCAATTTGTCACCC
Reference
Lu, X., et al. Multiple-integrations of HPV16 genome and altered transcription of viral oncogenes and cellular genes are associated with the development of cervical cancer. PLoS One ,2014,9(7): e97588.