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Sample GSM1588790 Query DataSets for GSM1588790
Status Public on Sep 15, 2015
Title Pt16-DP1-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi
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 16 melanoma, post BRAFi resistance, 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 0.869995551601424
cg00212031 0.199874882702534
cg00213748 0.317647058823529
cg00214611 0.194798572157063
cg00455876 0.601717464925012
cg01707559 0.193064836554091
cg02004872 0.0298325385383165
cg02011394 0.972442927484333
cg02050847 0.903568786982249
cg02233190 0.0504832146490336
cg02494853 0.0167195441064168
cg02839557 0.133286566117152
cg02842889 0.117112569409389
cg03052502 0.964343303581568
cg03155755 0.863962177825225
cg03244189 0.198272138228942
cg03443143 0.879265596462559
cg03683899 0.111446609936865
cg03695421 0.532392797475404
cg03706273 0.0235969041417856

Total number of rows: 485512

Table truncated, full table size 13835 Kbytes.

Supplementary file Size Download File type/resource
GSM1588790_9257625042_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588790_9257625042_R05C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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