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Sample GSM1588714 Query DataSets for GSM1588714
Status Public on Sep 15, 2015
Title Pt3-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 3 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 0.432077125328659
cg00212031 0.509267431597529
cg00213748 0.377799415774099
cg00214611 0.463850528025995
cg00455876 0.234100877192982
cg01707559 0.283796085571233
cg02004872 0.260801256873527
cg02011394 0.422165820642978
cg02050847 0.330835117773019
cg02233190 0.203389830508475
cg02494853 0.0249050604963349
cg02839557 0.231284916201117
cg02842889 0.461685823754789
cg03052502 0.464553794829024
cg03155755 0.509324009324009
cg03244189 0.327748263179403
cg03443143 0.483372003093581
cg03683899 0.254325259515571
cg03695421 0.373937677053824
cg03706273 0.0584309769535191

Total number of rows: 485512

Table truncated, full table size 13814 Kbytes.

Supplementary file Size Download File type/resource
GSM1588714_9283265061_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588714_9283265061_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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