TBC1D1 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004106
Fusion event
HPV-TBC1D1 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
E7
Start
612
Host Sequence
Chromosome
chr4
Cytoband
p14
Reference genome
GRCh37/hg19
Start
38117328/38115707 (Hg38)
End
38117328/38115707 (Hg38)
Location type
Exon16
Target gene
TBC1D1
miRNAs that regulate target gene
hsa-mir-125b-5p ; hsa-mir-193b-3p ; hsa-mir-7-1-3p ; hsa-mir-125a-5p ; hsa-mir-299-5p ; hsa-mir-548au-3p ; hsa-mir-449c-5p ; hsa-mir-34b-5p ; hsa-mir-2682-5p ; hsa-mir-3714
Nearest miRNA
hsa-mir-12113/Upstream/873716; hsa-mir-1243/Downstream/752325;
Nearest TSS
ENST00000502981/Upstream/3805; ENST00000475531/Downstream/193;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/100887, chr4-CpG: 164/Downstream/547321
Nearest cancer related gene
TBC1D1(OG, No orient, 0)
Upstream sequence
tgtacaaaacttacttcctgattgtccttgcctaaacaaaactgacttcctgattgtctgtctttgcctaaacacgcacacagtcttccctatttcaggc
Downstream sequence
AGGGCGAACCTTTCCTACACACCCATACTTCTCTGCCCAGCTTGGAGCAGGACAGCTATCGCTTTACAACATTTTGAAGGCCTACTCACTTCTAGACCAG
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