Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20000098
Fusion event
HPV-NFIB integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Gene
E2
Start
3647
Integrated sequence
GAATTGGAACAGGGTCGGGTACAGGCGGACGCACTGGGTATATTCCATTGGGAACAAGGCCTCCCACAGCTACAGATACACTTGCTCCTGTAAGACCCCC| |TTTAACAGTAGATCCTGTGGGCCCTTCTGATCCTTCTATAGTTTCTTTAGTGGAAGAAACTAGTTTTATTGATGCTGGTGCACCAACATCTGTACCTTCC
Host Sequence
Chromosome
chr9
Cytoband
p22.3
Reference genome
Start
End
14246496/14246497 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-372-3p ; hsa-mir-373-3p ; hsa-mir-130b-3p ; hsa-mir-124-3p ; hsa-mir-192-5p ; hsa-mir-93-5p ; hsa-mir-19b-3p ; hsa-mir-92a-3p ; hsa-mir-548c-3p ; hsa-mir-4668-3p ; hsa-mir-1277-5p ; hsa-mir-590-3p ; hsa-mir-19a-3p ; hsa-mir-130a-3p ; hsa-mir-301a-3p ; hsa-mir-519c-3p ; hsa-mir-519b-3p ; hsa-mir-519a-3p ; hsa-mir-454-3p ; hsa-mir-301b-3p ; hsa-mir-4295 ; hsa-mir-3666 ; hsa-mir-5011-5p ; hsa-mir-3714 ; hsa-mir-548aw ; hsa-mir-190a-3p ; hsa-mir-335-3p ; hsa-mir-8059 ; hsa-mir-4471 ; hsa-mir-1468-3p ; hsa-mir-548x-5p ; hsa-mir-548g-5p ; hsa-mir-548f-5p ; hsa-mir-548aj-5p ; hsa-mir-4517 ; hsa-mir-605-3p ; hsa-mir-20b-5p ; hsa-mir-519d-3p ; hsa-mir-526b-3p ; hsa-mir-17-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-20a-5p ; hsa-mir-6857-5p ; hsa-mir-491-5p ; hsa-mir-6769b-5p ; hsa-mir-6769a-5p ; hsa-mir-92a-2-5p ; hsa-mir-654-5p ; hsa-mir-541-3p ; hsa-mir-4451 ; hsa-mir-379-5p ; hsa-mir-3529-5p ; hsa-mir-4650-3p ; hsa-mir-4450 ; hsa-mir-3134 ; hsa-mir-6134 ; hsa-mir-1197 ; hsa-mir-6757-3p ; hsa-mir-3924 ; hsa-mir-656-3p ; hsa-mir-4775 ; hsa-mir-512-3p ; hsa-mir-4803 ; hsa-mir-302d-3p ; hsa-mir-302c-3p ; hsa-mir-302a-3p ; hsa-mir-302b-3p ; hsa-mir-302e ; hsa-mir-520b ; hsa-mir-520a-3p ; hsa-mir-520e ; hsa-mir-520d-3p ; hsa-mir-520c-3p ; hsa-mir-3912-5p ; hsa-mir-6748-3p ; hsa-mir-331-3p ; hsa-mir-6810-3p ; hsa-mir-6801-3p ; hsa-mir-605-5p ; hsa-mir-339-5p ; hsa-mir-6876-3p ; hsa-mir-626 ; hsa-mir-6773-3p ; hsa-mir-6893-3p ; hsa-mir-370-3p ; hsa-mir-1228-3p ; hsa-mir-3185 ; hsa-mir-1246 ; hsa-mir-129-5p ; hsa-mir-3672 ; hsa-mir-4524a-3p ; hsa-mir-6864-3p ; hsa-mir-8055 ; hsa-mir-431-5p ; hsa-mir-5691 ; hsa-mir-624-3p ; hsa-mir-6805-3p
Nearest miRNA
hsa-mir-101-2/Upstream/8238593; hsa-let-7a-1/Downstream/4326809;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/923146, chr9-CpG: 242/Downstream/66456
Nearest cancer related gene
NFIB(OG, No orient, 0)
Upstream sequence
cgggaacctgtaatcccagctactcaggaggctgaggcaggagaatcgcttgaacccaggaggcggaggttgcagtgagccaagatcacaccactgtaca
Downstream sequence
TTGATAGAATATCAAGTTTTGGCATAATGCCAAACTTTAATACTTCATATAGTACTTAGAAAATAGAAGGTGTTCAATTGATGAATGAATTAATAATTGA
Reference
Liu, Y., et al. Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology. Oncotarget,2016, 7(5): 5852-5864.