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Sample GSM1588788 Query DataSets for GSM1588788
Status Public on Sep 15, 2015
Title Pt16-baseline-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
Extracted molecule genomic DNA
Extraction protocol genomic DNA
Label Cy5 and Cy3
Label protocol Not provided
Hybridization protocol Not provided
Scan protocol Not provided
Description Patient 16 melanoma, pre MAPKi treatment, 1st biopsy
Data processing To identify the differentially methylated CpG sites, we analyze the Illumina 450K Methylation array output data using R-package minfi (Aryee et al., 2014). Raw image IDAT files were loaded into the R statistical computing environment using minfi, and the data was normalized using the SWAN function. This output a matrix of methylation indices (beta values), which were continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site. For each site, the methylation change was measured by the percent methylation difference (Δbeta) from paired baseline to DP/DD-DP samples. Minfi function dmpFinder was then applied to calculate the p-value of the logit transformed differential methylation. The p-values were corrected for multiple hypothesis testing with false discovery rates (FDR) q-values. We then used a cutoff of q-value ≤ 0.05 to define differential methylation
Submission date Jan 22, 2015
Last update date Sep 22, 2015
Contact name Willy Hugo
Organization name UCLA
Department Medicine
Street address 10833 Le Conte Ave, 52-121 CHS, Division of Dermatology
City Los Angeles
State/province California
ZIP/Postal code 90095
Country USA
Platform ID GPL13534
Series (2)
GSE65183 Methylation changes in pre MAPKi treatment and post MAPKi resistance Melanomas
GSE65186 Non-genomic and Immune Evolution in Melanoma with Acquired MAPKi Resistance

Data table header descriptions
VALUE Average Beta

Data table
cg00050873 0.826562451728506
cg00212031 0.13373063170441
cg00213748 0.548126064735945
cg00214611 0.143138111888112
cg00455876 0.584220036137322
cg01707559 0.127690383729349
cg02004872 0.0402619907418628
cg02011394 0.933990427901246
cg02050847 0.928151918559123
cg02233190 0.0815311418685121
cg02494853 0.0225606838125473
cg02839557 0.0904094010614102
cg02842889 0.0687081339712919
cg03052502 0.963631917272219
cg03155755 0.85270227054685
cg03244189 0.20046439628483
cg03443143 0.844070201250591
cg03683899 0.0513750954927426
cg03695421 0.606363907977293
cg03706273 0.0517543108981216

Total number of rows: 485512

Table truncated, full table size 13828 Kbytes.

Supplementary file Size Download File type/resource
GSM1588788_9257625042_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588788_9257625042_R04C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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