PBX1 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004032
Fusion event
HPV-PBX1 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
802
Host Sequence
Chromosome
chr1
Cytoband
q23.3
Reference genome
GRCh37/hg19
Start
164530806/164561569 (Hg38)
End
164530806/164561569 (Hg38)
Location type
Intron1
Target gene
PBX1
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-21-5p ; hsa-mir-877-3p ; hsa-mir-149-5p ; hsa-mir-196b-5p ; hsa-mir-198 ; hsa-mir-1247-3p ; hsa-mir-3074-5p ; hsa-mir-4722-3p ; hsa-mir-617 ; hsa-mir-6505-3p ; hsa-mir-6727-3p ; hsa-mir-6747-3p ; hsa-mir-6882-3p
Nearest miRNA
hsa-mir-101-1/Upstream/2218929; hsa-mir-1182/Downstream/1346352;
Nearest TSS
ENST00000473358/Upstream/1556; ENST00000474046/Downstream/1236;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/240039, chr1-CpG: 45/Downstream/14734
Nearest cancer related gene
PBX1(OG, No orient, 0)
Upstream sequence
gcagaggttgtagtgagcacagatcacgccactgctctctagcctgggctacagcgagactctgtctcaaaaaaaaaaaaGAGAGagaggcagagagagg
Downstream sequence
gtccaaagataaagattgtgatgactatgtagaatgttttcagactttagacatgaaataatttttagtttgacaaggtttagggcgcagccatgggagt
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