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Sample GSM1588766 Query DataSets for GSM1588766
Status Public on Sep 15, 2015
Title Pt10-DP4-1
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 10 melanoma, pre MAPKi treatment, 4th 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 0.871421380481973
cg00212031 0.136373436826218
cg00213748 0.610951008645533
cg00214611 0.10825774531747
cg00455876 0.652443014505399
cg01707559 0.117259620371331
cg02004872 0.0609058106258554
cg02011394 0.962022145541778
cg02050847 0.953826035983226
cg02233190 0.0470901485371948
cg02494853 0.0234155193181387
cg02839557 0.0645531355302302
cg02842889 0.0757556103255935
cg03052502 0.958685071221337
cg03155755 0.883535428919639
cg03244189 0.122093689153591
cg03443143 0.880383449636992
cg03683899 0.0383884454580008
cg03695421 0.674225191924936
cg03706273 0.031291129244538

Total number of rows: 485512

Table truncated, full table size 13822 Kbytes.

Supplementary file Size Download File type/resource
GSM1588766_9247377060_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588766_9247377060_R06C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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