GEO DataSets

(Submitter supplied) Hepatocellular carcinoma tumor samples were profiled for chromsomal copy number changes on Affymterix 100K SNP arrays

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL2005 GPL2004

40 Samples

Download data: CEL

(Submitter supplied) The molecular mechanisms whereby hepatitis B virus (HBV) induces hepatocellular carcinoma (HCC) remain elusive. We used genomic and molecular techniques to investigate host-virus interactions by mapping the entire liver of patients with HCC. We compared the gene signature of whole liver tissue (WLT) versus laser capture-microdissected (LCM) hepatocytes with intrahepatic expression of HBV. Gene expression profiling was performed on up to 17 WLT specimens obtained at various distances from the tumor center in individual livers of 11 patients with HCC and on selected LCM samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

140 Samples

Download data: CEL

(Submitter supplied) Purpose: Chronic Hepatitis B virus (HBV) infection leads to liver fibrosis which is a major risk factor in Hepatocellular carcinoma (HCC) and an independent risk factor of recurrence after HCC tumor resection. HBV genome can be inserted into human genome, and chronic inflammation may trigger somatic mutations. Several studies characterized HBV integration sites in HCC patients with regard to frequently occurring hotspots. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

42 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by genome tiling array

Platform:

GPL4091

64 Samples

Download data: TXT

(Submitter supplied) Purpose: To gain molecular insights of HBV integration that may contribute to HCC tumorigenesis, we performed whole transcriptome sequencing and whole genome copy number profiling of hepatocellular carcinoma (HCC) samples from 50 Chinese patients. Results: We identified a total of 33 HBV-human integration sites in 16 of 44 HBV-positive HCC tissues, which were enriched in HBV genotype C-infected patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

55 Samples

Download data: TXT

(Submitter supplied) Purpose: To gain molecular insights of HBV integration that may contribute to HCC tumorigenesis, we performed whole transcriptome sequencing and whole genome copy number profiling of hepatocellular carcinoma (HCC) samples from 50 Chinese patients. Conclusions: This is the first report on the molecular basis of the MLL4 integration driving MLL4 over-expression. HBV-MLL4 integration occurred frequently in Chinese HCC patients, representing a unique molecular segment for HCC with HBV infection.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

64 Samples

Download data: TXT

(Submitter supplied) Hepatitis B virus (HBV) infection is a major health problem worldwide and chronically infected individuals are at high risk of developing cirrhosis and hepatocellular carcinoma (HCC). The molecular mechanisms whereby HBV causes HCC are largely unknown. By using a biologically relevant system of HBV infection of primary human hepatocytes (PHHs), we studied how HBV perturbs gene expressions and signaling pathways of infected hepatocytes, and whether these effects are relevant to productive HBV infection and HBV-associated HCC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) Hepatocellular carcinoma (HCC) affects millions of people worldwide and is a lethal malignancy for which there are no effective therapies. To identify prognostic gene markers for liver cancer, we conducted transcriptome profiling of frozen tissues (tumor and non-tumor) from 300 early-to-advanced stage HCCs plus 40 cirrhotic and 6 normal livers.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10687

557 Samples

Download data: CEL

(Submitter supplied) Purpose: The goal of this study is to get a comprehensive evaluation of the transcriptome profile of HCC patients Methods:Transcriptome profiles of paired Tumor and adjacent non-tumour from 25 HCC patients were generated by deep sequencing using the Illumina HiSeq 2000 platform. Paired sample T-test was used to identify differentially expressed genes between Tumours and adjacent non-Tumours. Results: A total of 4462 genes are differentially expressed genes between tumours and adjacent non-tumours Conclusions: Characterization of the transcriptome profiles of HCC patients reveals key genes and pathways that are deregulated in HCC patients.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

52 Samples

Download data: XLSX

(Submitter supplied) We provide a comprehensive map of transcription start sites (TSSs) for HBV at single nucleotide resolution using CAGE.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112

11 Samples

Download data: BED

(Submitter supplied) To identify methylation levels of primary hepatoma (HCC) and cells We used microarray to detail the global programme of DNA methylation in HCC

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL18946

8 Samples

Download data: TXT

(Submitter supplied) Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We sequenced and analyzed the whole genomes of primary HCCs. To examine the influence of transcription-coupled repair (TCR) on somatic substitution patterns in HCC, we performed expression microarrays analysis and compared gene expression levels and the number of substitutions in 7 HCCs.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

7 Samples

Download data: TXT

(Submitter supplied) Hepatitis B virus (HBV) is known for its ability to interact with the host cell DNA methylation machinery. In HBV-infected hepatocytes, this interaction leads to chronic liver diseases, including hepatocellular carcinoma (HCC). We studied the extent of genomic changes induced by natural HBV infection in human primary hepatocytes. Transcriptome and methylome profiles were obtained at different time points post-infection to identify HBV-specific alterations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

20 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18694 GPL20084

35 Samples

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(Submitter supplied) Purpose: Chronic infection with hepatitis B virus is the leading global risk factor for the development of liver cancer. A large body of research has shown the many effects an HBV infection has on cellular physiology, particularly on pathways that may be involved in the development of HBV-associated diseases. Unfortunately, a significant portion of this research has been done in systems that may not mimic what is seen in a primary hepatocyte, and is not done on a transcriptome-wide scale. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20084

23 Samples

Download data: TXT

(Submitter supplied) Purpose: Chronic infection with hepatitis B virus is the leading global risk factor for the development of liver cancer. A large body of research has shown the many effects an HBV infection has on cellular physiology, particularly on pathways that may be involved in the development of HBV-associated diseases. Unfortunately, a significant portion of this research has been done in systems that may not mimic what is seen in a primary hepatocyte, and is not done on a transcriptome-wide scale. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

12 Samples

Download data: TXT