Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004524
Fusion event
HPV-HIF1A 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
2412
Integrated sequence
TATTACTATATGGTGCAGCTAACACAGGTA AATCATTATTTGGTATGAGTTTAATGAAATTTCTGCAAGGGTCTGTAATATGTTTTGTAAATTCTAAAA| |G CCATTTTTGGTTACAACCATTAGCAGATGCCAAAATAGGTATGTTAGATGATGCTACAGTGCCCTGTTGG AACTACATAGATGACAATTTAAGAAAT
Host Sequence
Chromosome
chr14
Cytoband
q23.2
Reference genome
Start
End
62135042/61668324 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-20a-5p ; hsa-mir-519c-3p ; hsa-mir-20b-5p ; hsa-mir-107 ; hsa-mir-18a-5p ; hsa-mir-17-5p ; hsa-mir-424-5p ; hsa-mir-199a-5p ; hsa-mir-138-5p ; hsa-mir-199b-5p ; hsa-mir-33a-5p ; hsa-mir-106b-3p ; hsa-let-7b-5p ; hsa-mir-210-3p ; hsa-mir-3121-3p ; hsa-mir-3668 ; hsa-mir-6815-3p ; hsa-mir-589-3p ; hsa-mir-889-3p ; hsa-mir-935 ; hsa-mir-1910-3p ; hsa-mir-3074-3p ; hsa-mir-5094 ; hsa-mir-6511a-5p ; hsa-mir-6755-5p ; hsa-mir-6806-5p ; hsa-mir-93-5p ; hsa-mir-106a-5p ; hsa-mir-106b-5p ; hsa-mir-519d-3p ; hsa-mir-4282 ; hsa-mir-8055 ; hsa-mir-153-5p ; hsa-mir-18b-5p ; hsa-mir-3662 ; hsa-mir-4735-3p ; hsa-mir-576-3p ; hsa-mir-151a-3p ; hsa-mir-5681b ; hsa-mir-155-5p ; hsa-mir-5692a ; hsa-mir-22-3p ; hsa-mir-21-5p ; hsa-mir-5089-3p ; hsa-mir-4662a-5p ; hsa-mir-1322 ; hsa-mir-509-5p ; hsa-mir-509-3-5p ; hsa-mir-4418 ; hsa-mir-6807-3p ; hsa-mir-217 ; hsa-mir-4799-5p ; hsa-mir-4463 ; hsa-mir-4499 ; hsa-mir-329-5p ; hsa-mir-4748 ; hsa-mir-4464 ; hsa-mir-449c-5p ; hsa-mir-34b-5p ; hsa-mir-2682-5p ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-6808-5p ; hsa-mir-106a-3p ; hsa-mir-299-5p ; hsa-mir-4470 ; hsa-mir-4487 ; hsa-mir-558 ; hsa-mir-3160-3p ; hsa-mir-3128 ; hsa-mir-625-3p ; hsa-mir-548ah-5p ; hsa-mir-3609 ; hsa-mir-494-3p ; hsa-mir-142-5p ; hsa-mir-27a-3p ; hsa-mir-433-3p ; hsa-mir-429 ; hsa-mir-338-3p ; hsa-mir-186-5p ; hsa-mir-138-1-3p ; hsa-mir-145-5p ; hsa-mir-200c-5p ; hsa-mir-497-3p
Nearest miRNA
hsa-mir-208a/Upstream/1019613; hsa-mir-1185-1/Downstream/2426700;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/345575, chr14-CpG: 112/Downstream/26805
Nearest cancer related gene
HIF1A(TSG, No orient, 0)
Upstream sequence
cagcagggattaggaggggtgtaaatacttggatagggctcttttccttggacttcctcacctccatcaacaggggtcaagaggagcctggacagtaatc
Downstream sequence
ccccttcttcagcctcattttctTGTTCATTGACTCattctttcattcaataagtgtttgctgaatgcccacactgtgtcaggtattggaccaaacactg
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.