GEO DataSets

(Submitter supplied) Serine-threonine kinase receptor-associated protein (STRAP) is upregulated in breast, colorectal and lung cancers, promoting their growth. We identify the upregulation of STRAP in hepatocellular carcinomas. Elevated STRAP endows tumor cells with growth advantage by reprograming a variety of metabolic processes and signaling pathways critical for hepatocellular carcinoma progression. Especially, enhanced Wnt/β-catenin signaling is likely to be a major effector of its tumor-promoting role.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: XLSX

(Submitter supplied) Mouse liver tumors (T) and non tumoral adjacent livers (NT) sorted from mice knock out for Axin1 gene specifically in the hepatocytes . 3 mice of the brother hood non deleted for Axin1 were used as controls (WT) We used microarrays to determine the differential expression between tumoral and non tumoral tissue.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL18802

16 Samples

Download data: CEL

(Submitter supplied) The goal of this study was to delineate the important EZH2 direct target genes that mediate the oncogenic properties of EZH2 in HCC. The EZH2 direct target genes in two HCC cell lines were identified by chromatin immunoprecipitation microarray (ChIP-chip) analysis and later confirmed by independent ChIP-PCR. The functions of the target genes were further examined.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4125 GPL4124

8 Samples

Download data: TXT

(Submitter supplied) Aberrant activation of Wnt/β-catenin signaling is observed in numerous cancers. In hepatocellular carcinoma activating mutations in CTNNB1 (20-25%) or loss of function mutations in AXIN1 (10%), AXIN2 (2%) and APC (1-2%) are observed. All these mutations lead to aberrant stabilization of β-catenin, which constitutively activates downstream Wnt/β-catenin target genes and triggers a genetic program resulting in tumor formation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) To identify pathways mediating the effects of Strap in colon cancer development, we established the mRNA expression profiles of intestinal adenomas that formed in ApcMin/+ mice with and without Strap deletion.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Up-regulation of canonical Wnt signaling has been implicated in liver fibrosis and cancer. To determine canonical Wnt target genes potentially implicated in these diseases, we performed microarray analysis of culture-activated rat hepatic stellate cells (HSCs) treated with canonical Wnt inhibitors, DKK-1, ICG-001, or FJ9.

Organism:

Rattus norvegicus albus; Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL6247

6 Samples

Download data: CEL

(Submitter supplied) Wnt/b-catening dependent HCC mouse models was used to assess microRNA profiles downstream of Wnt/b-catening pathway in mice HCC

Organism:

Mus musculus

Type:

Other

Platform:

GPL17873

6 Samples

Download data: TXT

(Submitter supplied) Wnt/b-catening dependent HCC mouse models was used to assess T-UCR profiles in mice HCC downstream of Wnt/b-catening pathway.

Organism:

Mus musculus

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL15691

6 Samples

Download data: TXT

(Submitter supplied) Normal human hepatocytes and 3 different HCC cell lines have been analyzed for the global expression of long non coding RNA (lncRNA). Total RNA was extracted from each sample using RNeasy Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed by Nanodrop ND-1000 and Bioanalyser2100. DNA microarray The Human Long Non-coding RNA Array was manufactured by Roche NimbleGen. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL11269

4 Samples

Download data: PAIR

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by SAGE

Platforms:

GPL570 GPL4

8 Samples

Download data: CEL, TAR

(Submitter supplied) We analyzed the level of DNA methylation by MeDIPseq in hepatocytes isolated by collagenase perfusion from Apclox/loxlivers, six days after injection of 2mg tamoxifen vs wt hepatocytes. Our aims was to study the impact of the beta-catenin on DNA methylation during the early steps of liver tumorigenesis

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BW

(Submitter supplied) Genomic analysis of human hepatocellular carcinoma (HCC) is potentially confounded by the differentiation state of the hepatic cell-of-origin. Here we integrated genomic analysis of mouse HCC (with defined cell-of-origin) along with normal liver development. We found a major shift in expression of Wnt and RXR-α pathway genes (up and down, respectively) coincident with the transition from hepatoblasts to hepatocytes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5818

Platform:

GPL7202

11 Samples

Download data: TXT

Analysis of hepatoblasts, immature hepatocytes and hepatocytes from livers at different developmental timepoints (embryonic day 14, embryonic day 18, post-natal day 5, post-natal day 56). Results provide insight into molecular mechanisms underlying normal liver development.

Organism:

Mus musculus

Type:

Expression profiling by array, log2 ratio, 4 age, 3 cell type, 2 development stage sets

Platform:

GPL7202

Series:

GSE65063

11 Samples

Download data: TXT

(Submitter supplied) Purpose:To understand the change in cellular metabolism and function for the overxepression of GSTZ1 or PCK1 in hepatoma cells. Methods:Total RNAs of AdGFP- , AdGSTZ1-, or AdPCK1-infected Huh7 cells were extracted using TRIzol (Invitrogen), following the manufacturer’s instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Novel Bio Ltd. Briefly, strand-specific RNA-seq libraries were prepared using the Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on Ion Torrent Proton sequencing platform. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

9 Samples

Download data: TXT

(Submitter supplied) Earlier studies linked sorafenib effectiveness to induction of ferroptosis. Herein we demonstrate sorafenib and mTKIs downregulate DDX5 in vitro and in vivo. To understand the effect of DDX5 downregulation, we compared TCGA-derived HCCs expressing low vs. high DDX5 focusing on ferroptosis-related genes. Glutathione Peroxidase 4 (GPX4), a key ferroptosis regulator, was significantly overexpressed in DDX5LOW HCCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) In the current study, we want to explore the crosstalk between NFE2L2 and beta-catenin.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: CSV, WIG

(Submitter supplied) We applied single-cell RNAseq analysis to characterize hepatic cell types, including hepatocytes (Hep) and non-parenchymal cells (NPC), in mouse liver, during Myc-induced hepatocellular carcinoma (HCC) development.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

18 Samples

Download data: H5

(Submitter supplied) Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, and prior attempts to develop genomic-based classification for HCC have yielded highly divergent results, indicating difficulty in identifying unified molecular anatomy. We performed a meta-analysis of gene expression profiles in data sets from eight independent patient cohorts across the world. In addition, aiming to establish the real world applicability of a classification system, we profiled 118 formalin-fixed, paraffin-embedded tissues from an additional patient cohort. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4269

Platform:

GPL3921

4 Samples

Download data: CEL

(Submitter supplied) Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, and prior attempts to develop genomic-based classification for HCC have yielded highly divergent results, indicating difficulty in identifying unified molecular anatomy. We performed a meta-analysis of gene expression profiles in data sets from eight independent patient cohorts across the world. In addition, aiming to establish the real world applicability of a classification system, we profiled 118 formalin-fixed, paraffin-embedded tissues from an additional patient cohort. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5474

118 Samples

Download data: TXT

Analysis of Hepatocellular carcinoma (HCC) Huh-7 cells stimulated with transforming growth factor-beta (TGF-β). HCC cell line Huh-7 has intact WNT pathway components. Results provide insight into the role of TGF-β in regulating WNT pathway activity in HCC cells.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 agent sets

Platform:

GPL3921

Series:

GSE10393

4 Samples

Download data: CEL