GEO DataSets

(Submitter supplied) The clinical course of prostate cancer (PCa) is highly variable, demanding an individualized approach to therapy and robust prognostic markers for treatment decisions. We here present a random forest-based classification model to predict aggressive behaviour of PCa. DNA methylation changes between PCa cases with good or poor prognosis (discovery cohort with n=78) were used as input. The model was validated with data from two independent PCa cohorts from ICGC and TCGA. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL18809

70 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: Global DNA methylation alterations are hallmarks of cancer. The tumor-suppressive TET enzymes, which are involved in DNA demethylation, are decreased in prostate cancer (PCa); in particular, TET2 is specifically targeted by androgen-dependent mechanisms of repression in PCa and may play a central role in carcinogenesis. Thus, identification of key genes targeted by TET2 dysregulation may provide further insight into cancer biology. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) DNA methylation analysis of paired prostate tumor and noncancerous tissues was perform in order to identify potential DNA methylation biomarkers for prostate cancer diagnostics and prognosis. Based on comparison of tumors versus noncancerous tissues and cases with and without biochemical disease recurrence (BCR), several gene targets were selected for more detailed analysis. Differences in methylation were further confirmed by means of methylation-specific PCR and significantly correlated with gene expression. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL19930

18 Samples

Download data: TXT

(Submitter supplied) Purpose: Clinicopathologic features and biochemical recurrence are sensitive, but not specific, predictors of metastatic disease and lethal prostate cancer. We hypothesize that a genomic expression signature detected in the primary tumor represents true biological potential of aggressive disease and provides improved prediction of early prostate cancer metastasis. Methods: A nested case-control design was used to select 639 patients from the Mayo Clinic tumor registry that underwent radical prostatectomy between 1987 and 2001. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

545 Samples

Download data: CEL, TXT

(Submitter supplied) Microarray-based DNA methylation and gene expression profiling was carried out using a panel of prostate cancer cell lines (LNCaP-FGC, DU-145, and PC-3) and the control normal prostate RWPE1 cell line. The identification of prostate cancer-specific methylation markers was based on the following criteria: a difference in DNA methylation level (β) of at least 0.5, and at least a 2-fold difference in expression level between cancer and control cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL6947 GPL8490

8 Samples

Download data: TXT

(Submitter supplied) TMEFF2 is an androgen regulated transmembrane protein mainly restricted to brain and prostate, that functions as a tumor suppressor in prostate cancer (PCa). Studies using publically available prostate cancer (PCa) datasets, reveal changes in the expression of TMEFF2 with disease stage, supporting an important role of TMEFF2 in this disease. However, the role of TMEFF2 in the biology and pathogenesis of PCa is still unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) The current methods to distinguish slow-growing from aggressive localised prostate cancer at diagnosis are imprecise so aggressive tumours can sometimes be missed. In this study we examined whether the changes in the features of cancer associated fibroblasts (CAFs) from the surrounding tumour microenvironment can help identify high risk tumours. We show that CAFs have a distinct methylation profile versus non-malignant prostate fibroblasts (NPFs) including specific differentially methylated regions that distinguish higher grade prostate cancer.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

41 Samples

Download data: IDAT, TXT

(Submitter supplied) Illumina M450 profiling was conducted on clinically-annotated human prostate cancer tissue and benign prostate tissue

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

136 Samples

Download data: TXT

(Submitter supplied) Here we used Illumina NGS for high-throughput profiling of the DNA methylome in seven human benign prostate tissues, seven human primary prostate cancer and six human castration resistant prostate cancer patient samples. These data were used to profile the CpG cytosine methylation pattern at single base resolution in each sample and to determine differentially methylated cytosines and regions among samples.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: TXT

(Submitter supplied) The clinical management of prostate cancer is challenging and currently relies primarily on staging, histological grading, and tumor size. In this study, we take advantage of the propensity of prostate cancer to be multifocal and categorize aggressiveness of individual prostate cancer foci based on DNA methylation patterns in primary and metastatic tumors.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

92 Samples

Download data: IDAT

(Submitter supplied) Clinical manifestation of PCa is highly variable. Aggressive tumors require radical treatment, while clinically non-significant ones may be suitable for active surveillance. We have previously developed the prognostic ProstaTrend signature mainly on prostatectomy specimens by application of transcriptome‐wide microarray and RNA-sequencing (RNA-Seq) analyses. We used a cohort of 185 tumor specimens obtained from FFPE biopsies for RNA-Seq to facilitate the application of ProstaTrend at the beginning of routine PCa diagnostic. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

176 Samples

Download data: CSV, TXT

(Submitter supplied) Genome-wide DNA methylation profiles were determined on a set of fresh 44 bladder cancer tissues using normal blood as control. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Agilent Human CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of bladder cancer along with finding markers for progresssion and early diagnosis.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL4126

44 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:

GPL10558 GPL13534

96 Samples

Download data

(Submitter supplied) Prognostic biomarkers are useful to screen patients with clinically localized prostate cancer (PCa) who are at high risk of metastatic progression. The tumor transcriptome can be used to evaluate the aggressiveness of PCa and predict adverse patient outcomes. Genomewide gene expression levels were measured in primary tumor samples of 503 patients in a population‐based cohort.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14951

503 Samples

Download data: IDAT, TXT

(Submitter supplied) Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated three PCa cell lines, 22Rv1, DU-145 and LNCap with the demethylating agent 5-aza 2’–deoxycitidine (DAC) and examined gene expression changes using a custom microarray (GPL16604). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16604

18 Samples

Download data: TXT

(Submitter supplied) We assessed transcriptome-wide gene expression in tissue specimens of PCa patients who underwent radical prostatectomy by next-generation sequencing (HiSeq 2000). We applied Cox proportional hazard models to the cohorts from different platforms and specimen types and combined the evidence from these by fixed effect meta-analysis to identify genes predictive for time to DoD (death of disease). Genes were combined by a weighted median approach into a prognostic score. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

40 Samples

Download data: GTF, TXT

(Submitter supplied) We assessed differential gene expression in tissue specimens of PCa and BPH patients who underwent radical prostatectomy by next-generation sequencing (HiSeq 2000). We stratified PCa patients according to seven clinical risk groups based on Gleason Score (GS), the presence of regional lymph node metastases (pN) and the occurrence of death of disease (DoD): (i) very low risk (group V: GS<7, pN0), (ii) low risk (group L: GS=7, pN0), (iii) medium risk (group M: GS<=7, pN1), (iv) high risk survivors without lymph node infiltration (group H-s: GS>7, pN0), (v) high risk non-survivors without lymph node infiltration (group H-d: GS>7, pN0, DoD), (vi) high risk survivors with lymph node infiltration (group H+s: GS>7, pN1), (vii) high risk non-survivors with lymph node infiltration (group H+d: GS>7, pN1, DoD). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

64 Samples

Download data: GTF, TXT

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumor, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

180 Samples

Download data: CEL, TXT

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16104

7 Samples

Download data: IDAT, TXT

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL20641

28 Samples

Download data: IDAT, TXT