Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004517
Fusion event
HPV-PTPRJ 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
3858
Integrated sequence
CATG GCATTGGACAGGACATAATGTAAAACATAAAAGTGCAATTGTTACACTTACATATGATAGTGAATGGCAA CGTGACCAATTTTTGTCTCAAGTT| |AAAATACCAAAAACTATTACAGTGTCTACTGGATTTATGTCTATAT GACAAATCTTGATACTGCATCCACAACATTACTGGCGTGCTTTTTGCTTTGCT
Host Sequence
Chromosome
chr11
Cytoband
p11.2
Reference genome
Start
End
47967861/47946309 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-328-3p ; hsa-mir-335-5p ; hsa-mir-124-3p ; hsa-mir-26b-5p ; hsa-mir-16-5p ; hsa-mir-31-5p ; hsa-mir-32-5p ; hsa-mir-92a-3p ; hsa-mir-205-5p ; hsa-mir-92b-3p ; hsa-mir-15a-5p ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-548c-3p ; hsa-mir-1277-5p ; hsa-mir-592 ; hsa-mir-376a-5p ; hsa-mir-4672 ; hsa-mir-597-5p ; hsa-mir-376a-2-5p ; hsa-mir-190b ; hsa-mir-190a-5p ; hsa-mir-936 ; hsa-mir-511-3p ; hsa-mir-5011-5p ; hsa-mir-6768-5p ; hsa-mir-4789-5p ; hsa-mir-3591-5p ; hsa-mir-190a-3p ; hsa-mir-142-3p ; hsa-mir-27b-5p ; hsa-mir-4280 ; hsa-mir-6516-3p ; hsa-mir-627-3p ; hsa-mir-3149 ; hsa-mir-1303 ; hsa-mir-5007-5p ; hsa-mir-505-3p ; hsa-mir-2278 ; hsa-mir-27a-5p ; hsa-mir-28-5p ; hsa-mir-299-3p ; hsa-mir-3139 ; hsa-mir-3158-3p ; hsa-mir-34a-5p ; hsa-mir-34c-5p ; hsa-mir-3688-5p ; hsa-mir-4265 ; hsa-mir-4266 ; hsa-mir-4296 ; hsa-mir-4322 ; hsa-mir-4417 ; hsa-mir-449a ; hsa-mir-449b-5p ; hsa-mir-548au-3p ; hsa-mir-6132 ; hsa-mir-6501-3p ; hsa-mir-6510-5p ; hsa-mir-6721-5p ; hsa-mir-6836-5p ; hsa-mir-708-5p ; hsa-mir-7106-3p ; hsa-mir-891a-3p
Nearest miRNA
hsa-mir-129-2/Upstream/545267; hsa-let-7a-2/Downstream/150473;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/97505, chr11-CpG: 177/Downstream/33743
Nearest cancer related gene
PTPRJ(TSG, No orient, 0)
Upstream sequence
GAACTACTCTAAGGATAACTATATGGGAAGTGTCAGTAAAGTTTACCATTTTGAGCTTCTTAAAGAATAACtatatatatatatatatatatatatatat
Downstream sequence
TGGAGCAAGTTGGTGTCATAAAAGCAATTGATTTGCTCTCCTGCTCTTGAACTCCTGTTTTCATTTAGGTACCTGGTAGAATGCTGGGTAATGAGAGAGT
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.