VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10018110

Fusion event

HBV-SAMD12 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

1631

Host Sequence

Chromosome

chr8

Cytoband

q24.12

Reference genome

GRCh37/hg19

Start

119363679/118351440 (Hg38)

End

119363679/118351440 (Hg38)

Location type

Intronic

Fragile sites / regions

FRA8C ; FRA8E

Target gene

SAMD12

miRNAs that regulate target gene

hsa-mir-340-5p ; hsa-mir-93-5p ; hsa-mir-526b-5p ; hsa-mir-570-3p ; hsa-mir-4635 ; hsa-mir-5584-3p ; hsa-mir-3976 ; hsa-mir-6856-5p ; hsa-mir-6758-5p ; hsa-mir-1277-5p ; hsa-mir-190a-3p ; hsa-mir-5011-5p ; hsa-mir-4520-2-3p ; hsa-mir-7156-5p ; hsa-mir-4273 ; hsa-mir-4520-3p ; hsa-mir-3144-3p ; hsa-mir-2117 ; hsa-mir-4720-3p ; hsa-mir-4804-3p ; hsa-mir-4645-3p ; hsa-mir-571 ; hsa-mir-6782-3p ; hsa-mir-875-5p ; hsa-mir-4796-3p ; hsa-mir-3609 ; hsa-mir-548ah-5p ; hsa-mir-144-3p ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-519d-3p ; hsa-mir-106a-5p ; hsa-mir-106b-5p ; hsa-mir-17-5p ; hsa-mir-526b-3p ; hsa-mir-20a-5p ; hsa-mir-20b-5p ; hsa-mir-302e ; hsa-mir-302a-3p ; hsa-mir-302b-3p ; hsa-mir-302c-3p ; hsa-mir-302d-3p ; hsa-mir-520d-3p ; hsa-mir-520c-3p ; hsa-mir-520a-3p ; hsa-mir-520b ; hsa-mir-520e ; hsa-mir-373-3p ; hsa-mir-372-3p ; hsa-mir-520f-3p ; hsa-mir-7850-5p ; hsa-mir-4529-3p ; hsa-mir-4535 ; hsa-mir-4776-5p ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-664b-3p ; hsa-mir-579-3p ; hsa-mir-659-5p ; hsa-mir-492 ; hsa-mir-6861-3p ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-3667-3p ; hsa-mir-6832-3p ; hsa-mir-6756-3p ; hsa-mir-4693-3p ; hsa-mir-539-5p ; hsa-mir-548n ; hsa-mir-5586-3p

Nearest miRNA

hsa-mir-12123/Upstream/1476640; hsa-mir-10400/Downstream/973731;

Nearest TSS

ENST00000518652/Upstream/60232; ENST00000625758/Downstream/28165;

Nearest CpG islands

None/Target, chr8-CpG: 109/Upstream/239216, chr8-CpG: 34/Downstream/270247

Upstream sequence

TGCTAATCAATTGCATCTGGCATGCGGAATGAAGCATATTTCACTAGGCTCCCCTCCTTCCCCACTCAGAGCCTTGGCCACTCATGTGTCCCCTTTTCAC

Downstream sequence

ggaacttgcccaaggtcctacagtagggagtggcagaactTCCTCTCTAGCTGCCTCAATCACAGCATTTACCTCATTGTGCTGTGGTCTGTCATGGTTT

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