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Sample GSM1588789 Query DataSets for GSM1588789
Status Public on Sep 15, 2015
Title Pt16-baseline-2
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 16 melanoma, pre MAPKi treatment, 1st biopsy, replicate
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 0.839354624085163
cg00212031 0.120465978289648
cg00213748 0.480015521924719
cg00214611 0.139973672663449
cg00455876 0.678762601777199
cg01707559 0.173299701046338
cg02004872 0.0407420249653259
cg02011394 0.948859543817527
cg02050847 0.929092750837641
cg02233190 0.0637474295391315
cg02494853 0.0291123256318687
cg02839557 0.114140698772427
cg02842889 0.146320893948977
cg03052502 0.961845574387947
cg03155755 0.838835666912307
cg03244189 0.224969528121191
cg03443143 0.851987457884589
cg03683899 0.0869340232858991
cg03695421 0.661571276217561
cg03706273 0.0448490184907029

Total number of rows: 485512

Table truncated, full table size 13819 Kbytes.

Supplementary file Size Download File type/resource
GSM1588789_9341679003_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588789_9341679003_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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