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Sample GSM1588727 Query DataSets for GSM1588727
Status Public on Sep 15, 2015
Title Pt5-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 5 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 0.540429217592147
cg00212031 0.633829301033949
cg00213748 0.513349946600214
cg00214611 0.0807840263784576
cg00455876 0.412177729018102
cg01707559 0.111502709370457
cg02004872 0.0325422069977979
cg02011394 0.643378381459607
cg02050847 0.553295546558704
cg02233190 0.040773024429407
cg02494853 0.0166376938073152
cg02839557 0.022698292532566
cg02842889 0.068749108543717
cg03052502 0.908217322642145
cg03155755 0.62286947958488
cg03244189 0.114169841464913
cg03443143 0.547370187337277
cg03683899 0.0436873345967291
cg03695421 0.402813619298321
cg03706273 0.030243044099857

Total number of rows: 485512

Table truncated, full table size 13834 Kbytes.

Supplementary file Size Download File type/resource
GSM1588727_8795207119_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588727_8795207119_R05C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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