Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004493
Fusion event
HPV-CLDN1 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
2080
Integrated sequence
CCTACGA TAATGACATAGTAGACGATAGTGAAATTGCATATAAATATGCACAATTGGCAGACACTAATAGTAATGCA AGTGCCTTTCTAAAAAGTAAT| |TCACAGGCAAAAATTGTAAAGGATTGTGCAACAATGTGTAGACATTATA AACGAGCAGAAAAAAAACAAATGAGTATGAGTCAATGGATAAAATATAGA
Host Sequence
Chromosome
chr3
Cytoband
q28
Reference genome
End
190056682/190338893 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-335-5p ; hsa-mir-375 ; hsa-mir-29b-3p ; hsa-mir-5100 ; hsa-mir-3942-3p ; hsa-mir-10b-3p ; hsa-mir-338-5p ; hsa-mir-3117-5p ; hsa-mir-376c-3p ; hsa-mir-7161-5p ; hsa-mir-548u ; hsa-mir-6858-5p ; hsa-mir-4689 ; hsa-mir-1224-5p ; hsa-mir-3915 ; hsa-mir-337-3p ; hsa-mir-642a-5p ; hsa-mir-6124 ; hsa-mir-3148 ; hsa-mir-3928-3p ; hsa-mir-4667-3p ; hsa-mir-4461 ; hsa-mir-1470 ; hsa-mir-3688-3p ; hsa-mir-141-5p ; hsa-mir-548c-3p ; hsa-mir-653-3p ; hsa-mir-4286 ; hsa-mir-1304-3p ; hsa-mir-5003-5p ; hsa-mir-1285-5p ; hsa-mir-1243 ; hsa-mir-142-5p ; hsa-mir-29a-3p
Nearest miRNA
hsa-let-7g/Upstream/508884; hsa-mir-3137/Downstream/4795613;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/16217, chr3-CpG: 71/Downstream/174648
Nearest cancer related gene
CLDN1(TSG, No orient, 0)
Upstream sequence
acttgtacaacatcctgcgtcactaagtTTGTGTTAGATGTTTTGATTGACTTAGAATCCATGTTCCTTCTTTCTTCATCTGTGGTTTCTGACCTACCCT
Downstream sequence
tcatacccctgcaggtcttggctgataactgctcaagttagcacatttcactgtagggttgtcctcagctgattgaagctacctcacccagaaatgcctg
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.