Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004526
Fusion event
HPV-SEMA4B 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
1028
Integrated sequence
TGGTTTTATGTAGAGGCTGTAGTGGAAAAAAAAACAGGGGATGCTATATCAGATGACGAGAACGA AAATGACAGTGATACAGGTGAAGATTTGGTAGAT| |TTTATAGTAAATGATAATGATTATTTAACACAGGCA GAAACAGAGACAGCACATGCGTTGTTTACTGCACAGGAAGCAAAACAACATAGAGATGCAGTA
Host Sequence
Chromosome
chr15
Cytoband
q26.1
Reference genome
Start
End
90729527/90186295 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-let-7e-5p ; hsa-mir-17-5p ; hsa-mir-20a-5p ; hsa-mir-93-5p ; hsa-mir-106b-5p ; hsa-mir-20b-5p ; hsa-mir-519d-3p ; hsa-mir-1236-3p ; hsa-mir-125a-5p ; hsa-mir-125b-5p ; hsa-mir-1273a ; hsa-mir-345-3p ; hsa-mir-3714 ; hsa-mir-4319 ; hsa-mir-4732-3p ; hsa-mir-605-3p ; hsa-mir-6515-3p ; hsa-mir-670-5p ; hsa-mir-6808-5p ; hsa-mir-6893-5p ; hsa-mir-940
Nearest miRNA
hsa-mir-10393/Upstream/179454; hsa-mir-1302-10/Downstream/2718104;
Nearest CpG islands
None/Target, chr15-CpG: 55/Upstream/957, chr15-CpG: 115/Downstream/14604
Upstream sequence
CAGCTCCTTTAATAAAATGTGTCAGTAATTTTAAGGTTTATAGTTCCCTCAACACAATTGCTAATGCAGAATAGTGTAAAATGCGCTTCAAGAATGTTGA
Downstream sequence
GCTCAAACTGTTGGTGACAGGTAATCTCCATATGGGGACATTggccaggcatggtggctcacgcctgtaatcccagcactttgggaggtcgaggcaggcg
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.