hsa-mir-4709-3p _HNSC.png
PHLDB2 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004038
Fusion event
HPV-PHLDB2 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
HPV33
Reference genome
Not given
Gene
E7
Start
846
Host Sequence
Chromosome
chr3
Cytoband
q13.2
Reference genome
GRCh37/hg19
Start
111496449/111777602 (Hg38)
End
111496449/111777602 (Hg38)
Location type
Intron1
Target gene
PHLDB2
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-1-3p ; hsa-mir-432-5p ; hsa-mir-376a-5p ; hsa-mir-382-3p ; hsa-mir-29c-3p ; hsa-mir-148a-3p ; hsa-mir-148b-3p ; hsa-mir-152-3p ; hsa-mir-202-5p ; hsa-mir-298 ; hsa-mir-4709-3p
Nearest miRNA
hsa-let-7g/Upstream/2174705; hsa-mir-12124/Downstream/335199;
Nearest TSS
ENST00000440867/Upstream/45105; ENST00000478922/Downstream/81578;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/102905, chr3-CpG: 59/Downstream/81788
Upstream sequence
gtaagggatggaaaaaaatattccacacaaacggaaaccaaaagtgtgcaaattagctatacttatatcagacaaaatagactttaaggcaaaaaaaaaa
Downstream sequence
TTCATCTTTATGTGATTTCTTTCTGTTATGTGCCACATTTTTTTTCTTCCAAAAGATACTCACTTGTGGTAACCCCATATGCATCATATTTGCAACTTGT
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