Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004537
Fusion event
HPV-GATAD2A 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
E5
Start
2132
Integrated sequence
AATTGGCAGACACTAATAGTAATGCA AGTGCCTTTCTAAAAAGTAATTCACAGGCAAAAATTGTAAAGGATTGTGCAACAATGTGTAGACATTATA AA| |CGAGCAGAAAAAAAACAAATGAGTATGAGTCAATGGATAAAATATAGATGTGATAGGGTAGATGATGG AGGTGATTGGAAGCAAATTGTTATGTTTTTA
Host Sequence
Chromosome
chr19
Cytoband
p13.11
Reference genome
Start
End
19610972/19500163 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-10a-5p ; hsa-mir-103a-3p ; hsa-mir-98-5p ; hsa-mir-16-5p ; hsa-mir-615-3p ; hsa-mir-92b-3p ; hsa-mir-92a-3p ; hsa-mir-1322 ; hsa-mir-5187-5p ; hsa-mir-1276 ; hsa-mir-4640-5p ; hsa-mir-4726-5p ; hsa-mir-548c-3p ; hsa-mir-4311 ; hsa-mir-211-3p ; hsa-mir-4648 ; hsa-mir-92b-5p ; hsa-mir-6739-5p ; hsa-mir-6733-5p ; hsa-mir-3153 ; hsa-mir-4745-5p ; hsa-mir-4328 ; hsa-mir-4481 ; hsa-mir-4681 ; hsa-mir-583 ; hsa-mir-4665-5p ; hsa-mir-1275 ; hsa-mir-4472 ; hsa-mir-4447 ; hsa-mir-92a-2-5p ; hsa-mir-5010-5p ; hsa-mir-7111-5p ; hsa-mir-4525 ; hsa-mir-6870-5p ; hsa-mir-5698 ; hsa-mir-4723-5p ; hsa-mir-625-5p ; hsa-mir-6845-5p ; hsa-mir-6762-5p ; hsa-mir-6825-5p ; hsa-mir-7106-5p ; hsa-mir-6797-5p ; hsa-mir-1249-5p ; hsa-mir-765 ; hsa-mir-6133 ; hsa-mir-6130 ; hsa-mir-6129 ; hsa-mir-6127 ; hsa-mir-4510 ; hsa-mir-4419a ; hsa-mir-4779 ; hsa-mir-4261 ; hsa-mir-3529-3p ; hsa-mir-1305 ; hsa-mir-1237-3p ; hsa-mir-1248 ; hsa-mir-15a-5p ; hsa-mir-15b-5p ; hsa-mir-18a-5p ; hsa-mir-18b-5p ; hsa-mir-1908-5p ; hsa-mir-195-5p ; hsa-mir-3180-3p ; hsa-mir-3180 ; hsa-mir-3196 ; hsa-mir-3612 ; hsa-mir-3908 ; hsa-mir-3925-3p ; hsa-mir-424-5p ; hsa-mir-4305 ; hsa-mir-4443 ; hsa-mir-4466 ; hsa-mir-4706 ; hsa-mir-4735-3p ; hsa-mir-4749-5p ; hsa-mir-4777-5p ; hsa-mir-4787-5p ; hsa-mir-4802-5p ; hsa-mir-497-5p ; hsa-mir-518d-5p ; hsa-mir-518e-5p ; hsa-mir-518f-5p ; hsa-mir-519a-5p ; hsa-mir-519b-5p ; hsa-mir-519c-5p ; hsa-mir-520c-5p ; hsa-mir-522-5p ; hsa-mir-523-5p ; hsa-mir-526a ; hsa-mir-589-3p ; hsa-mir-6502-3p ; hsa-mir-650 ; hsa-mir-663a ; hsa-mir-6730-5p ; hsa-mir-6753-5p ; hsa-mir-675-5p ; hsa-mir-6787-5p ; hsa-mir-6816-5p ; hsa-mir-6827-5p ; hsa-mir-6838-5p ; hsa-mir-6868-3p ; hsa-mir-744-5p ; hsa-mir-766-3p
Nearest miRNA
hsa-mir-10395/Upstream/65005; hsa-let-7e/Downstream/899109;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/93589, chr19-CpG: 26/Downstream/966
Upstream sequence
agatcaccttcgttagattccacatatgagtgagatcatgtgatatttgtctttctgtgcctcccttatttcacttaacacaatgttctctgagttcatc
Downstream sequence
CATCTCCTGACACCTCCCAGAGCCCCCAGCCTCGCACCATGTCTGGTTCTGGCGCCGCTCACGCTGGCCATGGGTTGGACGTGTGCAAGGAGATGTGCCG
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.