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.