Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004488
Fusion event
HPV-USP4 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
2574
Integrated sequence
GCCCTGTTGG AACTACATAGATGACAATTTAAGAAATGCATTGGATGGAAATTTAGTTTCTATGGATGTAAAGCATAGAC CATTGGTACAACTAAAAT| |GCCCTCCATTATTAATTACATCTAACATTAATGCTGGTACAGATTCTAGGTG GCCTTATTTACATAATAGATTGGTGGTGTTTACATTTCCTAATGAGT
Host Sequence
Chromosome
chr3
Cytoband
p21.31
Reference genome
Start
End
49319411/49281978 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
Nearest miRNA
hsa-mir-12127/Upstream/7792; hsa-let-7g/Downstream/524159;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/4596, chr3-CpG: 42/Downstream/57929
Nearest cancer related gene
USP4(OG, No orient, 0)
Upstream sequence
TTCATAGTtatgaagttttcagggcagagatttattatctctgaattggtaatgaagaaaaaactcaatgattaattaaactcagatagattaaattact
Downstream sequence
ctggcctggcgacagagtgagacacggtctcaaaaaaaaacaaaaacaaaacaaaaaaaaCAACAACAACAACAAAAGAAAATGGGAGAACCTTTCTGGG
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.