LINGO2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10015617
Fusion event
HBV-LINGO2 integration
Validated
No
Detection method
MAPS
Data source
Curated
Sample type
Tumor
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
chr9
Cytoband
p21.1
Reference genome
GRCh37/hg19
Start
28048670/28048672 (Hg38)
End
28048670/28048672 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA9C
Target gene
LINGO2
miRNAs that regulate target gene
hsa-mir-587 ; hsa-mir-7162-5p ; hsa-mir-516b-3p ; hsa-mir-516a-3p ; hsa-mir-2115-5p ; hsa-mir-1976 ; hsa-mir-6893-3p ; hsa-mir-370-3p ; hsa-mir-660-3p ; hsa-mir-5193
Nearest miRNA
hsa-mir-101-2/Upstream/6536487; hsa-let-7a-1/Downstream/814954;
Nearest TSS
ENST00000422679/Upstream/219396; ENST00000541043/Downstream/246659;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/474683, chr9-CpG: 74/Downstream/1163501
Upstream sequence
AATTATTCAACAAACAATATATGCACAGAAC
Junction sequence
AATTATTCAACAAACAATATATGCACAGAACAAGTTGCATGGTGCTGGTGAACAGACCAATTTATGTCTAGAGTCTGTTAGTACACAA
* 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.
Curate