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MBD-Chip Analysis

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. MBD-Chip Differential methylation.

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MBD-Chip Analysis

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  1. MBD-Chip Analysis Bioinformatics - Fish 546 Winter 2014

  2. 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

  3. MBD-Chip Differential methylation

  4. 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

  5. Microarray Data Processing • Read Nimblegenfiles 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

  6. Product – IGV xml

  7. Next Steps: Functional annotation • Further annotation of DMRs • DAVID, - Conserved Domain BLAST • Conserved Domain BLAST

  8. New Stuff! • Microarray analysis – Ryan Basom • Rpubs • IGV – making links to specific locations

  9. Bioinformatics though the ages… 2010 – MFG, GoogleDocs! 2013 – Galaxy, bedtools 2014 – R packages, reproducibility 2011 – no bisulfite aligners!

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