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Sample GSM1588704 Query DataSets for GSM1588704
Status Public on Sep 15, 2015
Title Pt1-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 1 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 0.873128714360942
cg00212031 0.17752875258036
cg00213748 0.505482456140351
cg00214611 0.197280966767372
cg00455876 0.613485934914506
cg01707559 0.116268866268866
cg02004872 0.0362888140665918
cg02011394 0.969036420646406
cg02050847 0.905393136008716
cg02233190 0.0795373665480427
cg02494853 0.0170169853703537
cg02839557 0.086360698125404
cg02842889 0.066973886328725
cg03052502 0.945763064751197
cg03155755 0.904912079510703
cg03244189 0.182649749188551
cg03443143 0.877521561308478
cg03683899 0.112955465587045
cg03695421 0.571766561514196
cg03706273 0.53718038195546

Total number of rows: 485512

Table truncated, full table size 13832 Kbytes.

Supplementary file Size Download File type/resource
GSM1588704_8795207135_R01C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588704_8795207135_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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