PRKCE _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018435
Fusion event
HBV-PRKCE 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
2966
Integrated sequence
CACCAGCAATCCTCTGGGATTCTTTCCCGACCACCAGTTGGATCCAGCCTTCAGAGCAAACACCGCAAATCCAGATTGGGACTTCAATCCCAACAAGGAC| |ACCTGGCCAGACGCCAACAAGGTAGGAGCTGGAGCATTCGGGCTGGGTTTCACCCCACCGCACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAGGGCA
Host Sequence
Chromosome
chr2
Cytoband
p21
Reference genome
GRCh37.55
Start
46344574/46117435 (Hg38)
End
46344574/46117435 (Hg38)
Location type
Intron11
Fragile sites / regions
FRA2S
Target gene
PRKCE
miRNAs that regulate target gene
hsa-mir-205-5p ; hsa-mir-1-3p ; hsa-mir-31-5p ; hsa-mir-96-5p ; hsa-mir-21-5p ; hsa-mir-342-3p ; hsa-mir-107 ; hsa-mir-146a-5p
Nearest miRNA
hsa-mir-1301/Upstream/10645949; hsa-mir-10b/Downstream/1260240;
Nearest TSS
ENST00000437798/Upstream/38607; ENST00000494472/Downstream/33618;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/464889, chr2-CpG: 289/Downstream/179215
Nearest cancer related gene
PRKCE(OG, No orient, 0)
Upstream sequence
CCTGTAATATCTCACTGTGACAGCAGGAGCATCCCAGCTGATCAGTAGGCTGGTGGGGGTCGCAGCAACAACTTCCAGGTCCCTCGGAACATCAGAAACT
Downstream sequence
TTTTCTGAGTTGGCTTTGAAATGATGGATTCTGAAATTAATTCTACATGAGGTCCAGAAATCACATGGGCAGAGATTTCCGGGCTCCCCATGGTACCTTC
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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