GEO DataSets

(Submitter supplied) Tumor suppressor genes (TSGs) are sometimes inactivated by transcriptional silencing through promoter hypermethylation. To identify novel methylated TSGs in melanoma, we carried out global mRNA expression profiling on a panel of 12 melanoma cell lines treated with a combination of 5-Aza-2-deoxycytidine (5AzadC) and an inhibitor of histone deacetylase, Trichostatin A. Reactivation of gene expression after drug treatment was assessed using Illumina whole-genome microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

24 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) Tumor angiogenesis requires intricate regulation of gene expression in endothelial cells (EC). We recently showed that DNA methyltransferase (DNMT)- and histone deacetylase (HDAC) inhibitors directly repress EC growth and tumor angiogenesis, suggesting that epigenetic modifications mediated by DNMTs and HDACs are involved in regulation of EC gene expression during tumor angiogenesis. To understand the mechanisms behind the epigenetic regulation of tumor angiogenesis, we used microarray analysis to perform a comprehensive screen to identify genes downregulated in tumor-conditioned versus quiescent EC, and re-expressed by 5-aza-2’-deoxycytidine and trichostatin A. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL885

4 Samples

Download data: TXT, XML

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL8490 GPL570

46 Samples

Download data: CEL

(Submitter supplied) Multiple DNA methylation changes have been associated with the acquisition of drug resistance; however it remains uncertain how many of these changes may represent critical DNA methylation drivers of chemoresistance. Using genome-wide DNA methylation profiling across 27,578 CpG sites on Illumina HumanMethylation27 bead array we identified loci at 4092 genes becoming hypermethylated in the chemoresistant A2780/cp70 ovarian tumour cell line compared to the parental sensitive A2780 line. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

31 Samples

Download data: TXT

(Submitter supplied) Multiple DNA methylation changes have been associated with the acquisition of drug resistance; however it remains uncertain how many of these changes may represent critical DNA methylation drivers of chemoresistance. Using gene expression profiling method on HGU133plus2 array, we identified a total of 1370 genes showing significant gene expression changes with 687 genes going up and 683 genes going down in the resistant (cp70) versus sensitive cell lines (A2780) by Rank Product (FDR<5%). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

15 Samples

Download data: CEL

(Submitter supplied) BACKGROUND: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

7 Samples

Download data: CEL

(Submitter supplied) Abstract Background: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The “rules” governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor-type specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype identify pathways important as therapeutic targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

42 Samples

Download data: CEL

(Submitter supplied) We performed a systematic, genome-wide screening of aberrantly methylated CGIs in stage I LADC from NS and S to identify tumor-associated genes commonly dysregulated through aberrant DNA methylation in early stage of LUAC regardless of smoking status. A series of criteria targeting novel genes frequently silenced in LADC tumors and cell lines possibly through hypermethylation were applied to prioritize the selection of top candidates for validation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

11 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to identify the gene affected carcinogenesis by DNA methylation in early lung adenocarcinoma

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

24 Samples

Download data: IDAT, TXT

(Submitter supplied) Epigenetic regulation of tumor suppressor genes (TSGs) has been shown to play a central role in melanomagenesis. Integrating gene expression and methylation array analysis we identified novel candidate TSGs frequently methylated in melanoma. We validated the methylation status of the most promising TSGs using the highly sensitive, specific and comprehensive Sequenom Epityper assay in a large panel of melanoma cell lines and resected melanomas, and compared the findings with that from cultured melanocytes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

12 Samples

Download data: TXT

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

Organism:

synthetic construct; Homo sapiens

Type:

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

Platforms:

GPL8786 GPL8019

69 Samples

Download data: CEL

(Submitter supplied) The contribution of aberrant DNA methylation and the downstream effects in tumorogenesis through silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations can be reversed, we investigated the effects of the epigenetic therapy in breast cancer cell lines. We used microarrays to investigate the global microRNA expression profile after demethylation treatment with 5-aza-2’-deoxycytidine (DAC) in breast cancer cell lines and identified distinct classes of early and late systematic stable or transient effects of the treatment.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8786

27 Samples

Download data: CEL

(Submitter supplied) The contribution of aberrant DNA methylation and the downstream effects in tumorogenesis through silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations can be reversed, we investigated the effects of the epigenetic therapy in breast cancer cell lines. We used microarrays to investigate the global gene expression profile after demethylation treatment with 5-aza-2’-deoxycytidine (DAC) in breast cancer cell lines and identified distinct classes of early and late systematic stable or transient effects of the treatment.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8019

42 Samples

Download data: CEL

(Submitter supplied) Purpose: The major aim of this study was to investigate the role of DNA methylation (referred to as methylation) on microRNA (miRNA) silencing in non-small cell lung cancers (NSCLC). Experimental Design: We performed microarray expression analyses of 856 miRNAs in NSCLC A549 cells before and after treatment with the DNA methyltransferase inhibitor 5-aza-2´-deoxycytidine (Aza-dC) and with a combination of Aza-dC and the histone deacetylase inhibitor trichostatin A. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8365

4 Samples

Download data: XLS

(Submitter supplied) Background: DNA methylation is an important component of epigenetic modifications that influences the transcriptional machinery and is aberrant in many human diseases. In particular, dysregulation of promoter methylation in cancer has already been shown to be associated with repression of tumor suppressors and activation of oncogenes. In addition, detection of altered promoter methylation status is suitable for the design of diagnostic or prognostic tests. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL6484 GPL6602

43 Samples

Download data: PAIR

(Submitter supplied) DNA methylation can contribute to the stable transcriptional silencing of mammalian genes. Oftentimes, these genes are important developmental regulators, and their silencing in cell types where they are not supposed to be active is important for the phenotypic stability of the cells. To identify key developmental regulator genes whose expression in terminally differentiated cells may be inhibited by DNA methylation, mouse dermal fibroblasts were demethylated with 5-aza-2’-deoxycytidine, and changes in gene expression monitored by microarray analysis. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Methylation profiling by array

Dataset:

GDS2044

Platform:

GPL1261

6 Samples

Download data

(Submitter supplied) To determine if aberrant activation of endothelin-1 (Et1) could lead to the dysregulation of many downstream genes, we exposed fibroblasts to exogenous ET1 peptide and assayed for transcriptional changes by microarray. Mouse dermal fibroblasts were treated with exogenous Et1 peptide for 24 hours. ET1 treatment resulted in significant expression changes — primarily downregulation — of a number of genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1980

Platform:

GPL1261

6 Samples

Download data: CEL, EXP

Analysis of primary dermal fibroblasts treated with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (Aza-dC) for 96 hours. This study seeks to identify developmental regulator genes whose expression in terminally differentiated cells is inhibited by DNA methylation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 agent sets

Platform:

GPL1261

Series:

GSE4696

6 Samples

Download data

Anlaysis of primary dermal fibroblasts treated with exogenous endothelin-1 (ET1) peptide for 24 hours. ET1 has been implicated in the pathogenesis of fibrotic and inflammatory diseases. Results suggest that stable silencing of Et1 is important for the phenotypic stability of dermal fibroblasts.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 agent sets

Platform:

GPL1261

Series:

GSE4695

6 Samples

Download data: CEL, EXP