Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004541
Fusion event
HPV-CBFA2T2 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
E1
Start
3888
Integrated sequence
CATAAAAGTGCAATTGTTACACTTACATATGATAGTGAATGGCAA CGTGACCAATTTTTGTCTCAAGTTAAAATACCAAAAACTATTACAGTGTCTACT| |GGATTTATGTCTATAT GACAAATCTTGATACTGCATCCACAACATTACTGGCGTGCTTTTTGCTTTGCTTTGTGTGCTTTTGTGTG TCTGCCTATTAA
Host Sequence
Chromosome
chr20
Cytoband
q11.22
Reference genome
Start
End
32116640/33528834 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-101-3p ; hsa-mir-106b-5p ; hsa-mir-92a-3p ; hsa-mir-7977 ; hsa-mir-7160-5p ; hsa-mir-5690 ; hsa-mir-4478 ; hsa-mir-4419b ; hsa-mir-3929 ; hsa-mir-510-5p ; hsa-mir-512-5p ; hsa-mir-1273g-3p ; hsa-mir-1910-3p ; hsa-mir-2467-3p ; hsa-mir-3202 ; hsa-mir-3714 ; hsa-mir-377-5p ; hsa-mir-4252 ; hsa-mir-4257 ; hsa-mir-4533 ; hsa-mir-455-3p ; hsa-mir-490-3p ; hsa-mir-5694 ; hsa-mir-605-3p ; hsa-mir-6086 ; hsa-mir-619-3p ; hsa-mir-6499-3p ; hsa-mir-6511a-5p ; hsa-mir-6516-5p ; hsa-mir-6807-5p
Nearest miRNA
hsa-mir-103a-2/Upstream/1290987; hsa-mir-1-1/Downstream/520285;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/38171, chr20-CpG: 17/Downstream/115530
Upstream sequence
TTAGGTTCAAGAGTTTGGATTTAAAACTGCAGTATTgtcaagtgcagtggctcacacctgtaatcccagctaccccggaggctgaggtgagaggaccgct
Downstream sequence
ggccTAAAATGTCAACTCTTGGTTGAGAATGAAGGCTAATTTGCCTAAGAACCAACTTAATCCATCTGTTCCAGCCAGTACCAAGTTTTGGGCTCGTGAT
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.