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Sample GSM1588752 Query DataSets for GSM1588752
Status Public on Sep 15, 2015
Title Pt9-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 9 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 0.457330415754923
cg00212031 0.376329787234043
cg00213748 0.291208791208791
cg00214611 0.504043126684636
cg00455876 0.219803370786517
cg01707559 0.347951807228916
cg02004872 0.327205882352941
cg02011394 0.397704253882512
cg02050847 0.276234567901235
cg02233190 0.156609195402299
cg02494853 0.0149642946843576
cg02839557 0.540876389797253
cg02842889 0.273212379935966
cg03052502 0.386322463768116
cg03155755 0.43310546875
cg03244189 0.309822866344605
cg03443143 0.342273307790549
cg03683899 0.250386398763524
cg03695421 0.239775910364146
cg03706273 0.0176624043108241

Total number of rows: 485512

Table truncated, full table size 13838 Kbytes.

Supplementary file Size Download File type/resource
GSM1588752_9257625042_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588752_9257625042_R04C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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