CSMD1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016367
Fusion event
HBV-CSMD1 integration
Validated
No
Detection method
WGS
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2012
PubMed ID
22267523
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
1568
End
1603
Orient
-
Integrated sequence
CTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCAC
Host Sequence
Chromosome
chr8
Cytoband
p23.2
Reference genome
GRCh37/hg19
Start
3732509/3874987 (Hg38)
End
3732544/3875022 (Hg38)
Orient
-
Location type
Intronic
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/1798347; hsa-mir-10400/Downstream/2747102;
Nearest TSS
ENST00000518652/Upstream/166491; ENST00000522905/Downstream/157078;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/852561, chr8-CpG: 256/Downstream/1116424
Nearby gene
MYOM2(-1639129) ; MCPH1(+2531603) ;
Nearest cancer related gene
CSMD1(TSG, No orient, 0)
Upstream sequence
gccatggagatttgggggttcatgtattactgcagtatatcctagcctatcttaaccaataAAacatgtaaagtactcaaagtgccagtgcctggcatac
Downstream sequence
cacaaaggctggcatgagctggggcggctgaaagagcagaagagcggacacagaaaggtgcctggggaccagatcctagaggggcttcaggaacacattg
Target sequence
TCTGGCTGCATCATCTCAAGAAGAATGGATGCAag
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