PDGFD _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018411
Fusion event
HBV-PDGFD integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2017
PubMed ID
29212479
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
1426
End
1869
Integrated sequence
TTACGTCCCGTCGGCGCTGAATCCTGCGGACGACCCTTCTCGGGGTCGCTTGGGACTCTCTCGTCCCCTTCTCCGTCTGCCGTTCCGACCGACCACGGGGCGCACCTCTCTTTACGCGGACTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCA
Host Sequence
Chromosome
chr11
Cytoband
q22.3
Reference genome
GRCh37.55
Start
104007729/104137001 (Hg38)
End
104007729/104137001 (Hg38)
Location type
Intron6
Target gene
PDGFD
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-145-5p
Nearest miRNA
hsa-mir-10392/Upstream/287021; hsa-let-7a-2/Downstream/7210756;
Nearest TSS
ENST00000527297/Upstream/99975; ENST00000527177/Downstream/27106;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/99739, chr11-CpG: 54/Downstream/26807
Upstream sequence
AGCTGAAGCATCAGAAGAAACAGATGAAAATGATTTGATCCTGGAAGTAACTGCAGGAGTTGGAGGTCAGGAGGCAATGTTGTTTACTTCAGAGATATTT
Downstream sequence
GATAGGTATCAGCAATATGCTGCATTTAAAAGATGACATTTTGAAACCCTGGAATATTTTCCAAGTGAAATAGGTGGCCGTAGACATGCGTCTGCCAGCA
Reference
Yoo, S., et al. A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC Med ,2017, 15(1): 214.
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