SMAD1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10015627
Fusion event
HBV-SMAD1 integration
Validated
No
Detection method
MAPS
Data source
Curated
Sample type
Adjacent tissue
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2012
PubMed ID
23236287
Virus Sequence
Virus name
HBV
Reference genome
AY800389.1;AY800390.1;AY800391.1;AY800392.1
Orient
-
Host Sequence
Chromosome
chr4
Cytoband
q31.21
Reference genome
GRCh37/hg19
Start
146451329/145530177 (Hg38)
End
146451329/145530177 (Hg38)
Orient
-
Location type
Intronic
Target gene
SMAD1
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-26a-5p ; hsa-mir-30a-5p ; hsa-mir-30b-5p ; hsa-mir-30c-5p ; hsa-mir-30d-5p ; hsa-mir-16-5p ; hsa-mir-205-5p ; hsa-mir-675-3p ; hsa-mir-3117-3p ; hsa-mir-216b-5p ; hsa-mir-3591-3p ; hsa-mir-21-3p ; hsa-mir-186-5p ; hsa-mir-26b-5p
Nearest miRNA
hsa-mir-12113/Upstream/2186642; hsa-mir-1305/Downstream/878406;
Nearest TSS
ENST00000502981/Upstream/4457; ENST00000511255/Downstream/14001;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/47346, chr4-CpG: 66/Downstream/88724
Upstream sequence
ACCCACAAAGGCATTACAGTCCAGGTGAAGTAAAGTCAACTTAGCAATAAAATGT
Junction sequence
ACCCACAAAGGCATTACAGTCCAGGTGAAGTAAAGTCAACTTAGCAATAAAATGTAGTTGCATGGTGCTGGTGAACACACCACTTTAT
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Ding, D., et al. Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach. PLoS Genet ,2010,8(12): e1003065.
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