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Sample GSM1588753 Query DataSets for GSM1588753
Status Public on Sep 15, 2015
Title Pt9-baseline-2
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, replicate
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 0.442607463391592
cg00212031 0.387769284225156
cg00213748 0.481173864894795
cg00214611 0.396632996632997
cg00455876 0.03847651180898
cg01707559 0.344843944575122
cg02004872 0.337823834196891
cg02011394 0.423738214087632
cg02050847 0.264501160092807
cg02233190 0.188222344523941
cg02494853 0.0239462669132678
cg02839557 0.439055520102106
cg02842889 0.452181856510435
cg03052502 0.360958904109589
cg03155755 0.547110552763819
cg03244189 0.345732314845566
cg03443143 0.449955713020372
cg03683899 0.235403151065802
cg03695421 0.201542416452442
cg03706273 0.0285140745471965

Total number of rows: 485512

Table truncated, full table size 13836 Kbytes.

Supplementary file Size Download File type/resource
GSM1588753_9341679003_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588753_9341679003_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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