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Series GSE27616 Query DataSets for GSE27616
Status Public on May 03, 2011
Title Agilent expression analysis of prostate cancer tissue samples
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample. While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6,691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer specific, including numerous novel DMRs. A novel cancer specific DMR in WFDC2 promoter showed heavy methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion positive and negative cancers. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression. In this submission, Agilent expression array data used for Gene Set Enrichment Analysis (GSEA) for enrichment analysis for gene repression is provided.
Overall design A total of 13 prostate tissue samples are hybridized against a benign prostate tissue sample pool obtained form a commercial source (Clontech Laboratories, Mountain View, CA) on Agilent Human GE 44k miroarray platform. The fold change between the average expression value from normal/benign (n = 4) and cancer samples (n = 9) was calculated and pre-ranked (representing 27,928 unique probes). This list was uploaded to GSEA, and enrichment analysis is performed using methylation target gene lists in tumor samples.
Contributor(s) Cao X, Jing X, Dhanasekaran SM, Kim JH, Chinnaiyan AM
Citation(s) 21724842
Submission date Mar 01, 2011
Last update date Feb 22, 2018
Contact name Jung Kim
Organization name University of Michigan
Street address 1400 E. Medical Center Drive
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
Platforms (1)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Samples (13)
GSM684559 Benign Prostate 1
GSM684560 Benign Prostate 2
GSM684561 Normal Prostate 1
This SubSeries is part of SuperSeries:
GSE27619 Deep sequencing reveals distinct patterns of DNA methylation and transcript isoform regulation in prostate cancer
BioProject PRJNA141771

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE27616_RAW.tar 190.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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