Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004501
Fusion event
HPV-RUNX2 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
3729
Integrated sequence
CAAAGGACGGATTAACTGTAATAGTAACACTACACCCATAGTACATTTAAAAGGTGATGCTA ATACTTTAAAATGTTTAAGATATAGATTTAAAAAGCA| |TTGTACATTGTATACTGCAGTGTCGTCTACATG GCATTGGACAGGACATAATGTAAAACATAAAAGTGCAATTGTTACACTTACATATGATAGTGAATG
Host Sequence
Chromosome
chr6
Cytoband
p12.3
Reference genome
Start
End
45659125/45691388 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-135b-5p ; hsa-mir-155-5p ; hsa-mir-335-5p ; hsa-mir-203a-3p ; hsa-mir-497-5p ; hsa-mir-195-5p ; hsa-mir-204-5p ; hsa-mir-433-3p ; hsa-mir-338-3p ; hsa-mir-124-3p ; hsa-mir-30d-5p ; hsa-mir-30a-5p ; hsa-mir-505-5p ; hsa-mir-484 ; hsa-mir-30b-5p ; hsa-mir-218-5p ; hsa-mir-23b-3p ; hsa-mir-34c-5p ; hsa-mir-30c-5p ; hsa-mir-205-5p ; hsa-mir-320a ; hsa-mir-135a-5p ; hsa-mir-222-3p ; hsa-mir-221-5p ; hsa-mir-628-3p ; hsa-mir-103a-3p ; hsa-mir-30a-3p ; hsa-mir-376c-3p
Nearest miRNA
hsa-mir-10398/Upstream/493618; hsa-mir-10524/Downstream/6452961;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/27311, chr6-CpG: 72/Downstream/323752
Nearest cancer related gene
RUNX2(TSG, No orient, 0)
Upstream sequence
aactcctgacctcgtgattcgctcacctcggcctcccaaagtgctgggattacaggcatgagccactgcgcctggccttttctgaatatttttgatccac
Downstream sequence
caatctgaggggaagaaaaggaattgcatataaacaaggcaaagtggtggccttaagggccaggatgaatgattgaggACATAGTGTGCACTCAGTGTTA
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.