GEO DataSets

(Submitter supplied) Epigenetic changes largely contribute to the regulation of gene expression in cancer cells. DNA methylation is part of the epigenetic gene regulation complex which is relevant for the pathogenesis of cancer. We performed a genome-wide search for methylated CpG islands in tumors and corresponding non-malignant lung tissue samples of 101 stage I-III non-small cell lung cancer (NSCLC) patients by combining methylated DNA immunoprecipitation and microarray analysis using NimbleGen´s 385K Human CpG Island plus Promoter arrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

18 Samples

Download data: CEL

(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:

GPL11013 GPL570

223 Samples

Download data: CEL, GFF, PAIR

(Submitter supplied) DNA methylation is an important mechanism for gene silencing in lung cancer. In this study we identified a large number of tumor specifically methylated genes in NSCLC patients by methylome profiling.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL11013

205 Samples

Download data: GFF, PAIR

(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: 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) PURPOSE: Non-small cell lung cancers (NSCLC) comprise multiple distinct biological groups with different prognoses. For example, patients with epithelial-like (EL) tumors have a better prognosis and exhibit greater sensitivity to inhibitors of the epidermal growth factor receptor (EGFR) pathway than patients with mesenchymal-like (ML) tumors. Here we test the hypothesis that EL NSCLCs can be distinguished from ML NSCLCs on the basis of global DNA methylation patterns. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

75 Samples

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(Submitter supplied) Non-small cell lung cancer (NSCLC) is a very common solid tumor where only small advances in the reduction of relapse-free survival and overall survival have been accomplished. The issue is particularly critical for stage I patients where there are not available biomarkers, in the absence of detectable nodal or other metastatic involvement, that might indicate which high-risk patients should receive the beneficially proved adjuvant chemotherapy. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

444 Samples

Download data

(Submitter supplied) Methylated genomic fragments from tumor and matching normal DNA were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. Samples from tumor were labeled with Cy5 while the matching normal were labeled with Cy3 so that methylation differences can be detected. Keywords: Cancer

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL4126

5 Samples

Download data: GPR

(Submitter supplied) Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

21 Samples

Download data: IDAT

(Submitter supplied) Comprehensive DNA methylation analysis in clinical samples of lung squamous cell carcinoma with or without tidiopathic pulmonary fibrosis. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 20 lung squamous cell carcinoma with or without tidiopathic pulmonary fibrosis and 13 surrounding lung samples.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

33 Samples

Download data: TXT

(Submitter supplied) The goal of the experiment – genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters Keywords: DNA methylation, Methylated CpG island amplification coupled with promoter arrays, normal tissue

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

4 related Platforms

4 Samples

Download data

(Submitter supplied) Understanding the molecular events in non-small cell lung cancer (NSCLC) is essential to improve early diagnosis and treatment for this disease. We examined the effect of chromosomal copy number changes on gene expression in resected NSCLC patients. We identified a deletion on 14q32.2-33 as a common alteration in NSCLC (44%), which significantly influenced gene expression for HSP90AA1, residing on 14q32. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL2827

32 Samples

Download data: XLS

(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:

GPL13534 GPL10558

253 Samples

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(Submitter supplied) Lung cancer is the worldwide leading cause of death from cancer. DNA methylation in gene promoter regions is a major mechanism of gene expression regulation that may promote tumorigenesis. Experimental Design Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 12 normal lung tissues and 124 tumors including 83 adenocarcinomas, 23 squamous cell carcinomas (SqCC), one adenosquamous cancer, five large cell carcinomas, nine large cell neuroendocrine carcinomas (LCNEC), and three small cell carcinomas (SCLC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

117 Samples

Download data: TXT

(Submitter supplied) Lung cancer is the worldwide leading cause of death from cancer. DNA methylation in gene promoter regions is a major mechanism of gene expression regulation that may promote tumorigenesis. However, whether clinically relevant subgroups based on DNA methylation patterns exist in lung cancer is not well studied. We performed whole-genome methylation analysis using 450K Illumina BeadArrays on 124 tumors including 83 adenocarcinomas, 23 squamous cell carcinomas, one adenosquamous cancer, five large cell carcinomas, nine large cell neuroendocrine carcinomas (LCNEC), three small cell carcinomas (SCLC) and 12 normal lung tissues. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

136 Samples

Download data: TXT, XLS

(Submitter supplied) Epigenetic changes through altered DNA methylation have been implicated with critical aspects of tumor progression, and have been extensively studied in cancer cells and tumor tissue samples. In contrast, our current knowledge of the aberrant genomic methylation in tumor-associated fibroblasts (TAFs), which are critical co-conspirators of tumor progression, is very scarce. To address this gap of knowledge, we conducted genome-wide DNA methylation profiling on lung TAFs and paired control fibroblasts (CFs) from surgical non-small cell lung cancer patients. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

28 Samples

Download data: TXT

(Submitter supplied) Small cell lung cancer (SCLC) is a disease characterized by aggressive clinical behavior and lack of effective therapy. Due to its high tendency of early dissemination, only a third of patients have limited-stage disease at the time of diagnosis. SCLC is thought to derive from neuroendocrine cells of the lung. Although several molecular abnormalities in SCLC have been described, there are relatively few studies on epigenetic alterations in this type of tumor. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL15160

29 Samples

Download data: GFF, PAIR

(Submitter supplied) Using paired tumor and non-tumor lung tissues from 47 individuals we identified common changes in DNA methylation associated with the development of non-small cell lung cancer. Pathologically normal lung tissue taken at the time of cancer resection was matched to tumorous lung tissue and together were probed for methylation status using Illumina GoldenGate arrays. For each matched pair the change in methylation at each CpG was calculated (the odds ratio), and these ratios were averaged across individuals and ranked by magnitude to identify the CpG’s with the greatest change in methylation associated with tumor development.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

94 Samples

Download data: TXT

(Submitter supplied) Methylated genomic fragments from tumor DNA and matching normal control were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. MIRA enriched samples from tumor were labeled with Cy5 while MIRA enriched DNA samples from normal tissue were labeled with Cy3. Keywords: Cancer

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL4126

6 Samples

Download data: GPR