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Sample GSM1588802 Query DataSets for GSM1588802
Status Public on Sep 15, 2015
Title Pt19-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 19 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 0.911166528124134
cg00212031 0.0678620689655172
cg00213748 0.457142857142857
cg00214611 0.116042780748663
cg00455876 0.765772195261205
cg01707559 0.238374801975585
cg02004872 0.0351783278113428
cg02011394 0.968841362999935
cg02050847 0.949924127465857
cg02233190 0.125514384737239
cg02494853 0.017696191779529
cg02839557 0.19855258550251
cg02842889 0.0522266262532059
cg03052502 0.962845968712395
cg03155755 0.871585028282585
cg03244189 0.080505860579889
cg03443143 0.912465584353935
cg03683899 0.0412907095903422
cg03695421 0.705082950935404
cg03706273 0.0140629760194978

Total number of rows: 485512

Table truncated, full table size 13832 Kbytes.

Supplementary file Size Download File type/resource
GSM1588802_9702496109_R01C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588802_9702496109_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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