Oyster DNA Methylation Analysis for Estrogen Response
Explore how DNA methylation mediates the oyster's response to estrogen using MBD-Chip bioinformatics approach with R packages. Learn about differential methylation, array design, microarray data processing, and next steps for functional annotation.
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Presentation Transcript
MBD-Chip Analysis Bioinformatics - Fish 546 Winter 2014
Overview Question: Is the oyster s response to estrogen (EE2) mediated by DNA methylation Approach: MBD-Chip Bioinformatics: R packages: Ringo, ChipPeakAnno Bedtools SQLshare DAVID
Array Design 3 x 720k design Methylation changes in response to EE2 Day 7 Control Pool: 3 females EE2 Pool: 3 females Input Pooled MBD (n=4) EE2: red cntrl: green EE2: green cntrl: red EE2: green cntrl: red
Microarray Data Processing Read Nimblegen files into R Remove control probes Loess normalize each array Smooth log2 ratio values by computing a running median Set a threshold for enriched regions Identify the overlap between replicates, and exclude regions where enrichment is present in control Evernote link
Next Steps: Functional annotation Further annotation of DMRs DAVID, - Conserved Domain BLAST Conserved Domain BLAST
New Stuff! Microarray analysis Ryan Basom Rpubs IGV making links to specific locations
Bioinformatics though the ages 2010 MFG, GoogleDocs! 2013 Galaxy, bedtools 2014 R packages, reproducibility 2011 no bisulfite aligners!
