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Sample GSM1588726 Query DataSets for GSM1588726
Status Public on Sep 15, 2015
Title Pt5-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 5 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 0.576562773594817
cg00212031 0.634078212290503
cg00213748 0.489655172413793
cg00214611 0.0832266325224072
cg00455876 0.431791907514451
cg01707559 0.15606392980257
cg02004872 0.045019804849773
cg02011394 0.67904476657298
cg02050847 0.550484363825499
cg02233190 0.0682552054336934
cg02494853 0.0321468233093693
cg02839557 0.0451952119923929
cg02842889 0.0696324951644101
cg03052502 0.91873792659369
cg03155755 0.647572045474575
cg03244189 0.12561797752809
cg03443143 0.574745370812711
cg03683899 0.102291597475922
cg03695421 0.445365572826713
cg03706273 0.0318065259839556

Total number of rows: 485512

Table truncated, full table size 13812 Kbytes.

Supplementary file Size Download File type/resource
GSM1588726_8795207135_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588726_8795207135_R01C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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