Moore Notes 3 30 15

Group Call

• Participants: Katie, Tom, Patrick, Stacia, Dongying

• Shotmap paper in review, but no updates

• MicrobeCensus is published at Genome Biology

• CAMI competition (assembly, taxonomic annotation of assemblies, binning)
  • Humann2 potentially with MicrobeCensus
  • PhyloSift

• Patrick: variable (and stable) gene families across metagenomes (slides)
  • Linear model for log abundance of gene family with study effects
  • Test statistic is variance of residuals (for each gene family)
  • Tom: be cautious about low abundance families (need 100 reads for accurate mean estimate)
    • Patrick did use only universally present families, which tend to be fairly abundant
  • Unmapped reads (%) affects overall abundance for all families
  • JE: how to get from gene family abundance to pathways/functions?
    • Patrick: for now just doing enrichment tests
    • Correlation of families might predict shared functions
  • Testing if residual variance is larger than expected given mean abundance
    • Bootstrap null with centering and scaling (estimated by Poisson)
  • Normalizing for gene length and average genome size
  • Overlaying with phylogenetic breadth data
    • Two component signaling pathways have small PD, but are very stable (e.g., quorum sensing, sporulation)
    • Tom: sample PD vs. database PD
    • JE: Does KEGG have many families of unknown function
      • Repeat on SFAMs novel gene families to get a hit list (Stacia) and covariation with known genes

• Next Calls:
  • April 13: Tom and Tara Oceans
  • April 27: Stacia novel gene families