GEO DataSets

(Submitter supplied) PGG is a natural product exhibits anti-cancer effects on different type of cancers including liver cancer cell lines. In present study we identified a set of genes affected by PGG treatment in Huh7 cells. Some of them, for example, control cell cycle and cell proliferation. We used microarrays to delineate the mechnism of action of PGG on GNMT expression in HCC. We identified distinct classes of up-regulated and down-regulated genes after PGG treatment in Huh7 cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

9 Samples

Download data: CEL

(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:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

250 Samples

Download data: CEL

(Submitter supplied) We report that 7 of 7 female Gnmt-/- mice developed hepatocellular carcinoma (HCC), the most common form of liver cancer, at the mean age of 16.1 months. In contrast, only one-third (2/6) of male Gnmt-/- mice had HCC, the remaining had either premature death or liver necrosis. Microarray analysis showed that genes involved in the following pathways were deregulated in different stages of tumorigenesis: S-adenosylmethionine (SAM)-dependent methyltransferases, metabolism, signal transduction, cell proliferation, cell adhesion and immune responses. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

10 Samples

Download data: CEL

(Submitter supplied) Hepatocellular carcinoma (HCC), the main form of liver cancer, is the sixth most common cancer and the third most frequent cause of cancer death worldwide1. The exact mechanism of HCC initiation and development is still unclear, though inflammation has been shown to play a key role in this progression. Herein, we performed a gene expression assay to screen for alterative expression of genes among normal liver tissues, HCC tissues and its paracancer tissues with hepatitis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17077

9 Samples

Download data: TXT

(Submitter supplied) We compared miRNA expression profiles among 5 groups of HepG2 cells treated with various concentrations (0,100,200 nM) of triptolide for 12 h or 24 h.

Organism:

Rattus norvegicus; Human alphaherpesvirus 2; Merkel cell polyomavirus; Mus musculus cytomegalovirus 2; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1

Type:

Non-coding RNA profiling by array

Platform:

GPL11434

15 Samples

Download data: GPR, TXT

(Submitter supplied) Purpose: The goals of this study are to use RNA-seq-derived JHH-7 cell transcriptome profiling for differentially expressed genes after PRMT5 knockdown. Methods: mRNA profiles of control and PRMT5 knockdown JHH-7 cells were generated by RNA-seq, using Illumina Novaseq 6000.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat2 or HISAT2. The gene expression quantification was performed using RSEM tool and generated raw count for all genes individually. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV

(Submitter supplied) Liver cancer is one of the leading causes of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC) is the most common liver cancer, and limited therapeutic options are available. Here we discovered that urinary dimethylarginine, especially symmetric dimethylarginine (SDMA), was found to be increased in HCC in a MYC-dependent manner. Mechanistically, protein arginine methyltransferase 5 (Prmt5), which was highly induced in HCC, is a direct MYC target gene. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: TXT

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

Organism:

Rattus norvegicus; Mus musculus

Type:

Expression profiling by array; Expression profiling by RT-PCR

Platforms:

GPL22525 GPL11533

69 Samples

Download data: CEL, TXT

(Submitter supplied) BACKGROUND & AIMS: We performed an integrated analysis to identify microRNAs (miRNAs) and mRNAs with altered expression in liver tumors from 3 mouse models of hepatocellular carcinoma (HCC) and human tumor tissues. METHODS: We analyzed miRNA and mRNA expression profiles of liver tissues from mice with diethylnitrosamine-induced hepatocarcinogenesis, conditional expression of lymphotoxin alpha and lymphotoxin beta , or inducible expression of a Myc transgene (Tet-O-Myc mice), as well as male C57BL/6 mice (controls). more...

Organism:

Rattus norvegicus; Mus musculus

Type:

Expression profiling by RT-PCR

Platform:

GPL22525

34 Samples

Download data: TXT

(Submitter supplied) BACKGROUND & AIMS: We performed an integrated analysis to identify microRNAs (miRNAs) and mRNAs with altered expression in liver tumors from 3 mouse models of hepatocellular carcinoma (HCC) and human tumor tissues. METHODS: We analyzed miRNA and mRNA expression profiles of liver tissues from mice with diethylnitrosamine-induced hepatocarcinogenesis, conditional expression of lymphotoxin alpha and lymphotoxin beta , or inducible expression of a Myc transgene (Tet-O-Myc mice), as well as male C57BL/6 mice (controls). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11533

35 Samples

Download data: CEL

(Submitter supplied) Background & Aims. Glycine N-methyltransferase (GNMT) is an essential regulator of the total transmethylation flux in the mammalian liver. Distinct DNA methylation patterns are characteristic of liver development, hepatic de-differentiation and liver disease progression, processes in which the levels of GNMT decrease dramatically by mechanisms still poorly understood. Interestingly, putative binding sites for the microRNA miRNA-873-5p were identified in the 3´UTR of GNMT suggesting a potential role for miRNA-873-5p in GNMT regulation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16173

13 Samples

Download data: TSV

(Submitter supplied) We performed RNA-seq on HeLa cells treated with MYCASO-3, a non-targeting ASO (NT-ASO), Lipofectamine alone, and untreated cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

21 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

93 Samples

Download data: BED

(Submitter supplied) Tumors driven by activation of the transcription factor Myc generally show oncogene addiction. However, the gene-expression programs that depend upon sustained Myc activity in those tumors remain unknown. We have addressed this issue in a model of liver carcinoma driven by a reversible tet-Myc transgene, combining gene expression profiling with the mapping of Myc and RNA Polymerase II on chromatin. Switching off the oncogene in advanced carcinomas revealed that Myc is required for the continuous activation and repression of distinct sets of genes, constituting no more than half of those deregulated during tumor progression, and an even smaller subset of all Myc-bound genes. We further showed that a Myc mutant unable to associate with the co-repressor protein Miz1 is defective in the initiation of liver tumorigenesis. Altogether, our data provide the first detailed analysis of a Myc-dependent transcriptional program in a fully developed carcinoma, revealing that the critical effectors of Myc in tumor maintenance must be included within defined subsets (ca. 1,300 each) of activated and repressed genes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

46 Samples

Download data: CSV

(Submitter supplied) Tumors driven by activation of the transcription factor Myc generally show oncogene addiction. However, the gene-expression programs that depend upon sustained Myc activity in those tumors remain unknown. We have addressed this issue in a model of liver carcinoma driven by a reversible tet-Myc transgene, combining gene expression profiling with the mapping of Myc and RNA Polymerase II on chromatin. Switching off the oncogene in advanced carcinomas revealed that Myc is required for the continuous activation and repression of distinct sets of genes, constituting no more than half of those deregulated during tumor progression, and an even smaller subset of all Myc-bound genes. We further showed that a Myc mutant unable to associate with the co-repressor protein Miz1 is defective in the initiation of liver tumorigenesis. Altogether, our data provide the first detailed analysis of a Myc-dependent transcriptional program in a fully developed carcinoma, revealing that the critical effectors of Myc in tumor maintenance must be included within defined subsets (ca. 1,300 each) of activated and repressed genes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

47 Samples

Download data: BED

(Submitter supplied) We generated liver-specific Dyrk2 knockout mice mating Dyrk2 flox mice with Alb-cre mice and co-introduced SB13-transposase-, myrAkt-, Myc- and mutant Hras-expressing plasmids with either HA- or Dyrk2-expressing plasmid into the knockout mice by HTVi. Dyrk2-expressing suppressed tumorigenesis compared with HA-expressing.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL20258

6 Samples

Download data: CEL

(Submitter supplied) Cancer cells vary in their nutritional dependencies, thus characterization of nutrient demand of each tumor type is needed to uncover specific vulnerabilities. We demonstrate that MYC-driven liver tumors rely on increased tryptophan (Trp) uptake to grow. By following 13C-Trp in vivo-labeling, we found that Trp catabolism is reduced while its incorporation into proteins is increased in tumors. Trp deprivation prevents MYC-driven tumors from arising, as well as the growth of xenografted cells while minimally affecting normal cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT