hsa-mir-338-5p _HNSC.png
CSMD1 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003894
Fusion event
HPV-CSMD1 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
L1
Start
823
Host Sequence
Chromosome
chr8
Cytoband
p23.2
Reference genome
GRCh37/hg19
Start
2944617/3087095 (Hg38)
End
2944617/3087095 (Hg38)
Location type
Exon49
Target gene
CSMD1
miRNAs that regulate target gene
hsa-mir-297 ; hsa-mir-3924 ; hsa-mir-190a-3p ; hsa-mir-4789-5p ; hsa-mir-567 ; hsa-mir-5011-5p ; hsa-mir-4704-5p ; hsa-mir-5583-3p ; hsa-mir-4517 ; hsa-mir-1277-5p ; hsa-mir-338-5p ; hsa-let-7c-3p ; hsa-mir-10b-5p
Nearest miRNA
hsa-mir-3674/Upstream/1010455; hsa-mir-10400/Downstream/3535029;
Nearest TSS
ENST00000518652/Upstream/43307; ENST00000522905/Downstream/20060;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/64669, chr8-CpG: 256/Downstream/1904351
Nearest cancer related gene
CSMD1(TSG, No orient, 0)
Upstream sequence
CCTTCCATGGTGTGACCAGATCAGCCTTGGGGCCGAATGAGAGCCACATCATTCTTGCCATTCATCGAGCGTGGTTCTGCTGCACAAACAGGTGAATTAC
Downstream sequence
CCCTGGCAGAGTGGCGTGAGGGAGTCCCACTGGTACATGCCAAGTGGGTTTCGTCTACAGGTTGCATTGCTGTGGCCGACCATTCGGTATCCAGGCTTGC
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