CSMD1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018208
Fusion event
HBV-CSMD1 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2017
PubMed ID
28622513
Virus Sequence
Virus name
HBV
Reference genome
Not given
Start
1020
Host Sequence
Chromosome
chr8
Cytoband
p23.2
Reference genome
GRCh37/hg19
Start
4018111/4160589 (Hg38)
End
4018111/4160589 (Hg38)
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/2083949; hsa-mir-10400/Downstream/2461535;
Nearest TSS
ENST00000518652/Upstream/128489; ENST00000522905/Downstream/834112;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/1138163, chr8-CpG: 256/Downstream/830857
Nearest cancer related gene
CSMD1(TSG, No orient, 0)
Upstream sequence
GTCTGGCAGAAGGGTGGGCAGTTTAAGAAGATCTCTGCCACAGTCAAAGATTGGGGATTCTTTAGAAATATCACATTTTCATTTCACAAAAAATAATTCC
Downstream sequence
CTCCATTTACACACTGTGGATGTCCCCACTTTCTTGCAGACACTCTGGAAGTCTTTGTACTTGTGTGTGCACAGACACATGTCCACGCAATGTCCCACAC
Reference
Cancer Genome Atlas Research Network. Electronic address, w. b. e. and N. Cancer Genome Atlas Research . Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell ,2017,169(7): 1327-1341 e13
Curate