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Sample GSM1588734 Query DataSets for GSM1588734
Status Public on Sep 15, 2015
Title Pt6-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 6 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 0.856481736543441
cg00212031 0.426337448559671
cg00213748 0.537481259370315
cg00214611 0.220167327168648
cg00455876 0.704903417533432
cg01707559 0.182916616820194
cg02004872 0.0451081612586037
cg02011394 0.953448445332722
cg02050847 0.928014998996673
cg02233190 0.510657484833579
cg02494853 0.0312540980023604
cg02839557 0.103340496190662
cg02842889 0.105755395683453
cg03052502 0.949697851387646
cg03155755 0.895629352982739
cg03244189 0.310663308144416
cg03443143 0.882473148940215
cg03683899 0.10796766743649
cg03695421 0.664847512038523
cg03706273 0.0450460147462462

Total number of rows: 485512

Table truncated, full table size 13821 Kbytes.

Supplementary file Size Download File type/resource
GSM1588734_9513149079_R01C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588734_9513149079_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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