ARHGEF3 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003852
Fusion event
HPV-ARHGEF3 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
162
Host Sequence
Chromosome
chr3
Cytoband
p14.3
Reference genome
GRCh37/hg19
Start
57074785/57040757 (Hg38)
End
57074785/57040757 (Hg38)
Location type
Intron1
Target gene
ARHGEF3
miRNAs that regulate target gene
hsa-mir-138-5p ; hsa-mir-373-3p ; hsa-mir-335-5p ; hsa-mir-769-5p ; hsa-mir-377-5p ; hsa-mir-485-5p ; hsa-mir-3680-3p ; hsa-mir-557 ; hsa-mir-507 ; hsa-mir-450b-5p ; hsa-mir-889-3p ; hsa-mir-4793-5p ; hsa-mir-5196-3p
Nearest miRNA
hsa-let-7g/Upstream/1188163; hsa-mir-12124/Downstream/3577048;
Nearest TSS
ENST00000440867/Upstream/63382; ENST00000334325/Downstream/19684;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/238575, chr3-CpG: 112/Downstream/37964
Upstream sequence
gtgggaggatcacttgaaccctaggagtttgaggctgcagtgaactatgatcatgccactgccctccagcctgggtggacagagcaagaccctctctctt
Downstream sequence
CAGGCCTGTGTCCTTTCACCTCTGAATGAAGCAGACCCCAGCTGACCTCCTCAACACCCACACCACCCTGCCAACCGCTGCCCACCAGACTGACCTGGAA
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