hsa-mir-378g _HNSC.png
hsa-mir-1278 _HNSC.png
BCAS3 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003853
Fusion event
HPV-BCAS3 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
28928286
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Not given
Gene
E4
Start
847
Host Sequence
Chromosome
chr17
Cytoband
q23.2
Reference genome
GRCh37/hg19
Start
59151118/61073757 (Hg38)
End
59151118/61073757 (Hg38)
Location type
Intron20
Target gene
BCAS3
miRNAs that regulate target gene
hsa-mir-1278 ; hsa-mir-1285-3p ; hsa-mir-2861 ; hsa-mir-3187-5p ; hsa-mir-326 ; hsa-mir-330-5p ; hsa-mir-3664-5p ; hsa-mir-3667-3p ; hsa-mir-378g ; hsa-mir-4486 ; hsa-mir-4714-5p ; hsa-mir-514a-5p ; hsa-mir-5189-5p ; hsa-mir-612 ; hsa-mir-6734-3p ; hsa-mir-6860 ; hsa-mir-6883-3p
Nearest miRNA
hsa-mir-10226/Upstream/1030652; hsa-mir-1250/Downstream/1870458;
Nearest TSS
ENST00000595228/Upstream/3401; ENST00000588008/Downstream/4684;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/395638, chr17-CpG: 720/Downstream/321942
Upstream sequence
TCGACCTTTTCTTTCTTTCTGATCCCTCTTGCTGTGGTCTGATGCTTCTGAATTCTTCCAAGGGTCATCTTATTTTTGAATTCTTCCTCTTCGTCTAACT
Downstream sequence
TTACCTCCCCTCTTTTTCTCTGTTCCTCCCAGTACTTCATTGCTTGATTTCTCTGAGTATTAAAATGGTAggccaggcgtggtggttcatgcctgtaatc
Reference
Koneva, L. A., et al. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res ,2018,16(1): 90-102.
Curate