Kun:LabNotes/CpgSeq/2009-8-31

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Data analysis on the cpg97k data from a pair of whole blood samples from a Breast cancer patient[edit]

  • The experiment was performed by Jie.
  • The read mapping to the whole genome was performed with Robert's program.
   Samples                 50192A        50192B
   # raw reads           10,401,608    9,693,893
   # Cpg site called       60,039        52,501
  • There are 45,851 sites that were covered at least 10x in both samples.
  • 800 sites are significantly different between the two samples (x2>10.84, |A-B|>=0.1). These sites are associated with 504 genes.
  • None of the Nrf2 targets were differentially methylated.
  • Genes that are less methylated in 50192B are enriched for the regulation of metabolic process.
  • Genes that are more methylated in 50192B are "Biological process", but not to any more specific category.