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Sample GSM1588826 Query DataSets for GSM1588826
Status Public on Sep 15, 2015
Title Pt23-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 23 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 0.89071016975549
cg00212031 0.0987213454671121
cg00213748 0.64853195164076
cg00214611 0.0538804638715433
cg00455876 0.797297778727801
cg01707559 0.138623251402829
cg02004872 0.0618231680038965
cg02011394 0.972645153959777
cg02050847 0.956250280734852
cg02233190 0.148508137432188
cg02494853 0.0341329687279923
cg02839557 0.0492767835253739
cg02842889 0.131167763157895
cg03052502 0.953270411193981
cg03155755 0.925465838509317
cg03244189 0.281433607520564
cg03443143 0.922158124399083
cg03683899 0.0468487094610199
cg03695421 0.795742387496632
cg03706273 0.323080029615669

Total number of rows: 485512

Table truncated, full table size 13815 Kbytes.

Supplementary file Size Download File type/resource
GSM1588826_9513149079_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588826_9513149079_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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