Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006337
Fusion event
HBV-LMLN integration
Validated
Yes
Detection method
invPCR +Sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1844
Integrated sequence
CGCCGACGGGACGTAAACAAAGGACGTCCCGCGCAGGATCCAGTTGGCAGCACAGCCTAGCAGCCATGGAAACGATGTATATTTGCGGGATAGGACAACA| |GAGTTATCAGTCCCGATAATGTTTGCTCCAGACCTGCTGCGAGCAAAACAAGCGGCTAGGAGTTCCGCAGTATGGATCGGCAGAGGAGCCGAAAAGGTTC
Host Sequence
Chromosome
chr3
Cytoband
q29
Reference genome
Start
End
197990949 (Hg38)
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-192-5p ; hsa-let-7e-5p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-95-5p ; hsa-mir-130a-3p ; hsa-mir-301a-3p ; hsa-mir-130b-3p ; hsa-mir-374a-5p ; hsa-mir-454-3p ; hsa-mir-301b-3p ; hsa-mir-4295 ; hsa-mir-3666 ; hsa-mir-4671-3p ; hsa-mir-6083 ; hsa-mir-217 ; hsa-mir-548a-3p ; hsa-mir-548e-3p ; hsa-mir-548f-3p ; hsa-mir-2116-3p ; hsa-mir-548ar-3p ; hsa-mir-548av-3p ; hsa-mir-548az-3p ; hsa-mir-6807-3p ; hsa-mir-4473 ; hsa-mir-3074-3p ; hsa-mir-944 ; hsa-mir-875-5p ; hsa-mir-5582-3p ; hsa-mir-4446-5p ; hsa-mir-6794-3p ; hsa-mir-215-3p ; hsa-mir-6773-3p ; hsa-mir-1304-3p ; hsa-mir-6814-5p ; hsa-mir-4639-3p ; hsa-mir-3664-5p ; hsa-mir-3184-3p
Nearest miRNA
hsa-let-7g/Upstream/316373;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/30486, chr3-CpG: 160/Downstream/89209
Downstream sequence
AATGACNGATNATTTTCTTTGGT
Junction sequence
TTTCACNTCTGCCTAATCATTCAATGACNGATNATTTTCTTTGGT
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
Reference
Mason, W. S., et al. HBV DNA Integration and Clonal Hepatocyte Expansion in Chronic Hepatitis B Patients Considered Immune Tolerant. Gastroenterology,2016, 151(5): 986-998 e984.