CSMD1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016051
Fusion event
HBV-CSMD1 integration
Validated
Yes
Detection method
Alu PCR and sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2012
PubMed ID
22962577
Virus Sequence
Virus name
HBV
Reference genome
Not given
Start
1826
Orient
+
Host Sequence
Chromosome
chr8
Cytoband
p23.2
Reference genome
GRCh37/hg19
Start
3679736/3822214 (Hg38)
End
3679736/3822214 (Hg38)
Orient
-
Location type
Intron
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/1745574; hsa-mir-10400/Downstream/2799910;
Nearest TSS
ENST00000518652/Upstream/113718; ENST00000522905/Downstream/209886;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/799788, chr8-CpG: 256/Downstream/1169232
Nearest cancer related gene
CSMD1(TSG, No orient, 0)
Upstream sequence
CACTTCGGATTTGATCAGATCTAATTTCATTCACGTGGTAGGTGCCACGCTGACAATAAAGCATTATGGGCTGTCAGTCTACTTAGATTTCAATTCTGTA
Downstream sequence
TCTGCCATGTGCCTGCTTCCATCACTTAACCTCTGGACGCATCCCTTAAAGAGACATTTACCCTTGTAAGAGCTTGTGTCTAGGGGGAAGAACAGGTGTT
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.
Curate