Moore Notes 3 2 15

From OpenWetWare
Jump to navigationJump to search

Group Call

  • Participants: Katie, Tom, Dongying, Sarah, Stephen, Patrick, Guillaume, Josh
  • Shotmap manuscript ready to submit
    • Reviewers / conflicts of interest
    • Corresponding author
  • Dongying: slides
    • Phylogenetic profiling of gene families
      • Presence/absences indicates functional relationship
      • Correlation assumes independence of lineages, which is not true
      • Independent contrasts approach corrects for dependence but creates errors
      • Solution uses TreeOTU at different cutoffs and looks at correlation over range of phylogenetic levels
      • Analyzed ~8K genomes and 9K PfamA families
        • Different patterns of loss/gain across lineages and Pfams
        • Many Pfams come and go across phylogeny
        • Identified core genes with consistent presence/absence
        • SPICi clustering of Pfams using average distance at 3 semi-independent phylogenetic levels
    • Next steps:
      • Maximum likelihood ancestral state reconstruction (vs. Felsenstein 1985)
      • Other protein databases
      • Visualization
    • Katie: Gold standards for true and false positives
    • Tom: what is gained versus using overall correlation (i.e., not using tree)?
    • Patrick: Is this a special case of TIC (phylogenetic regression), e.g., with weights?
  • Future calls
    • March 16: Tara Oceans
    • March 30: Patrick
    • April 13: TBD