Moore Notes 7 30 14

Group Call

• Participants: Katie, Tom, Dongying, Guillaume, Sarah, Stacia, Stephen, Josh, Patrick

• MMI event at San Jose tonight

• Shotmap functional analysis
  • Analyzed L4 and MetaHIT
  • Results: slides
  • Functional diversity vs. phenotypes
    • Kegg KO Shannon entropy low in Crohn's disease (CD) metagenomes
      • 3-group tests (CD, UC, healthy) not significant, but CD significantly lower than healthy
    • SFams richness and Shannon entropy low in CD
      • How accurately can we estimate richness?
      • Diversity may be correlated with BMI because both are low in CD
  • Principal components analysis
    • Center and scale or not?
    • Families with high loadings on PCs (ECF factors, iron membrane receptor)
  • Testing for significant differences in abundance between groups
    • Families with lowest q-values
    • Check if family names have error
  • Need to compare across databases
  • Comparison to taxonomic profiles
  • Differentiation from MG-RAST, humann, etc.
    • M5NR is pretty diverse
    • But shotmap allows a custom db (should show this, e.g., Morgan et al findings, extended metaCyc)
  • Link to simulations
  • Review literature on MetaHIT re-analyses
  • Strength is a tool that works and simulations to evaluate it and optimize

• Upcoming calls:
  • Aug 6: Stephen
  • Aug 13: Patrick - biomarkers
  • Aug 20: Josh/Tom - allergens
  • Aug 27: Dongying - phyeco