GEO DataSets

(Submitter supplied) Introduction: Hepatocellular carcinoma (HCC) is one of the most aggressive solid tumors and oncogenic pathways (e.g Akt, IGF signaling) are often activated in high proliferating HCC. Among several genetic alterations, epigenetic changes seem to be involved in the development and progression of HCC. DNA hypermethylation of promoter regions is almost always associated with transcriptional silencing and can lead to inactivation of tumor suppressor genes (TSG) in cancer cells. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

102 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of paired adjacent and hepatocellular samples and 8 non-diseased liver samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 12 paired adjacent and 12 hepatocellular samples.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

32 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL4126 GPL4133

20 Samples

Download data: TXT

(Submitter supplied) The analysis of DNA methylation profiles was performed by methylated DNA immunoprecipitation (MeDIP) using anti-5-methylcytidine antibody (Eurogentec, Seraing, Belgium) followed by the Human 244K Agilent CpG island microarray (Agilent, Santa Clara, CA)

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL4126

4 Samples

Download data: TXT

(Submitter supplied) Gene expression was profiled using a 4x44K Human Whole Genome Ver. 2.0 gene expression array (Agilent Technologies) according to the manufacturer's instructions (Microarray-based gene expression analysis protocol ver. 5.0.1, Agilent Technologies)

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

16 Samples

Download data: TXT

(Submitter supplied) 61 human HCCs were analyzed for genome-wide gene expression. Samples were collected at two sites in Germany, Heidelberg (HD) and Hannover (N). The Heidelberg Collection include 40 independent HCC: 19 liver resections and 17 explant liver specimen (4 not determined); median age at surgery was 57 years (range, 16-78), and the male/female ratio was 3:1. All diagnoses were confirmed by histological reevaluation, and use of the samples was approved by the local ethics committee. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

80 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of primary HCC tumors and their non-tumor tissue counterparts. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 20 paired tumor and non-tumor tissues which were obtained from HCC patients who underwent surgery.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

40 Samples

Download data: TXT

(Submitter supplied) Background: C3H mice have been frequently used in cancer studies as animal models of spontaneous liver tumors and chemically induced hepatocellular carcinoma (HCC). Epigenetic modifications, including DNA methylation, are among pivotal control mechanisms of gene expression leading to carcinogenesis. Although information on somatic mutations in liver tumors of C3H mice is available, epigenetic aspects are yet to be clarified. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLSX

(Submitter supplied) We have employed microarray analysis to detect tumor-related genes of liver tissues in C3H mice

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

6 Samples

Download data: TXT

(Submitter supplied) To analysis Mst1r and slpi function as a tumor associated gene, we carried out overexpression analysis of Mst1r or Slpi to Hepa1c1c7 and investigated downstream genes expression by microarray.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

3 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL13534 GPL10558

68 Samples

Download data: IDAT

(Submitter supplied) For the AcceSssIble assay, nuclei preparation and M.SssI methyltransferase (New England BioLabs) treatment were performed. The subsequent Infinium DNA methylation assay was performed at the University of Southern California Molecular Genomics Core Facility according to the manufacturer’s specifications (Illumina).

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

34 Samples

Download data: IDAT, TXT

(Submitter supplied) There is an urgent need for developing more effective therapies for aggressive hepatocellular carcinoma (HCC). Guadecitabine (SGI-110) is a second-generation DNA methyltransferase inhibitor (DNMTi) currently in clinical trials for HCC and shows greater stability and performance over first generation DNMTis. The aim of this study is to identify potential therapeutic targets of SGI-110 for clinical trials.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

34 Samples

Download data: IDAT, TXT

(Submitter supplied) Chromatin plasticity can be exploited therapeutically for the selective manipulation of the epigenetic state, to ultimately restore transcriptional aberrations driving tumorigenesis. Abnormal epigenetic silencing of tumor suppressors genes (TSGs) is one of the carcinogenesis features in hepatocellular carcinoma (HCC). We computationally identified a panel of 12 putative TSGs exhibiting an anti-correlation between transcript abundance and promoter DNA methylation, while harbouring no genetic alterations. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

16 Samples

Download data: IDAT, TXT

(Submitter supplied) Non-coding microRNAs (miRNAs) mainly regulate the expression of targeted genes by regulating mRNA degradation or repressing their protein translation. MiRNA microarray profiling was then performed on 218 human HCC tumors samples, 10 samples from adjacent cirrhotic non-tumoral tissue, 10 samples from healthy liver and 12 HCC cell lines. In this study we investigated which miRNAs were differentially expressed in HCC compared to cirrhotic non-tumoral tissue and healthy liver.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

250 Samples

Download data: CEL

(Submitter supplied) Genome-wide expression analysis of 228 hepatocellular carcinoma and 168 cirrhotic samples as part of a integrated study of gene expression and DNA-methylation de-regulation in patients with hepatocellular carcinoma Analysis of whole-genome transcriptome changes in human samples from hepatocellular carcinoma patients

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

396 Samples

Download data: CEL

(Submitter supplied) Genome-wide DNA methylation profiling of cirrhosis and dysplastic liver samples. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,577 CpGs sites. Samples included 130 cirrhosis and 8 exhibiting dysplasia. The manuscript includes an integrative analysis of these samples along with samples from normal liver and HCC already deposited under GSE63898.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

138 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are aberrant expressed in hepatocellular carcinoma (HCC) tissue and play a central role in diverse biological processes. We conducted a genome-wide miRNAs screening in 10 pairs of HCC tumor and adjacent non-tumor tissues to test the hypothesis that dysregulation of miRNAs in HCC tumor tissue are partially due to aberrant methylation in relevant miRNAs host genes. Taqman low density arrays were used to examine miRNA profiles in paired HCC tissues, and quantitative RT-PCR was used to validate candidate miRNAs for both discovery and validation sets.

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL18262

20 Samples

Download data: TXT

(Submitter supplied) We examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared to non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

132 Samples

Download data: CSV

(Submitter supplied) BACKGROUND & AIMS: In approximately 70% of patients with hepatocellular carcinoma (HCC) treated by resection or ablation, disease recurs within 5 years. Although gene expression signatures have been associated with outcome, there is no method to predict recurrence based on combined clinical, pathology, and genomic data (from tumor and cirrhotic tissue). We evaluated gene expression signatures associated with outcome in a large cohort of patients with early stage (Barcelona-Clinic Liver Cancer 0/A), single-nodule HCC and heterogeneity of signatures within tumor tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18461

69 Samples

Download data: TXT