VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20003970

Fusion event

HPV-KLF12 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

E6

Start

743

Host Sequence

Chromosome

chr13

Cytoband

q22.1

Reference genome

GRCh37/hg19

Start

74311491/73737354 (Hg38)

End

74311491/73737354 (Hg38)

Location type

Intron6

Fragile sites / regions

FRA13E

Target gene

KLF12

miRNAs that regulate target gene

hsa-mir-101-3p ; hsa-mir-23a-3p ; hsa-mir-4652-3p ; hsa-mir-4743-3p ; hsa-mir-218-5p ; hsa-mir-4679 ; hsa-mir-4677-3p ; hsa-mir-216b-5p ; hsa-mir-1264 ; hsa-mir-6888-3p ; hsa-mir-4775 ; hsa-mir-215-3p ; hsa-mir-6773-3p ; hsa-mir-34a-5p ; hsa-mir-141-3p ; hsa-mir-137 ; hsa-mir-200a-3p ; hsa-mir-4720-3p ; hsa-mir-4804-3p

Nearest miRNA

hsa-mir-1297/Upstream/7519030; hsa-mir-1267/Downstream/3960658;

Nearest TSS

ENST00000623511/Upstream/89101; ENST00000419499/Downstream/257695;

Nearest CpG islands

None/Target, chr13-CpG: 551/Upstream/677122, chr13-CpG: 31/Downstream/396618

Upstream sequence

gcaagaccctgtctcaaaagaaaGGGAACATGCTGTTTAGTTAGTAGTATGACAAAGCATTTATCTACATGTAATTTAAAAGATATCATTCAATACAATG

Downstream sequence

GACAACAAAAGTCGGTGCCTCCATTATGTTcatggtaattagagggatttcgaggaagatgtcgccccctaggggctctggtggtcaggaagtcatcctg

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.