Moore Notes 1 15 14

Group Call

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

• PICRUSTs update http://edhar.genomecenter.ucdavis.edu/~gjospin/picrust_test/picrust_test/Jan_13_2014_modules/
  • Found a bug in mapping from Kegg Orthology Groups to Modules, but fixing it did not change results
    • Modules better correlated than individual KOs, but still not highly correlated between PICRUSTs and Shotmap
  • Fixing this made it run faster (now don't search all family members, just the module ID)
  • Ran full data set plus top 100
    • Correlations a bit higher for top 100
    • However residuals are pretty large
  • How bad would PICRUSTs output be for niche modeling
    • Josh recommends looking at logic transformed relative abundances
  • Patrick: could be useful to look at KO (or module) across samples to see if correlated between PICRUSTs and Shotmap
  • Let's put this on hold for now, and see how long it takes for metagenomic data to come
  • Patrick might want to apply PICRUSTs to estimate protein family abundances in mammalian microbiomes with metabolomics data

• EFI collaboration
  • They do all analyses based on UniProt IDs (vs. genomes)
    • KB database as source of input sequences for current analysis pipeline
  • How many Sfams have no Pfam annotation?
    • Annotated Pfams: ~61% of Sfams have no Pfam
    • Pfam-B families (unannotated): TBD
  • What percent of InterPro has an Sfam?
    • For comparison, only ~19% of InterPro (UniProtKB) has no Pfam
  • Should annotate and score families
    • Jonathan: should use metrics to score these (phylogenetic breadth), not just family size
    • Tom: also how connected is Sfam in family network space
    • Stephen: from gut (genomes plus assembled proteins), consistently present, maybe correlated with a phenotype
    • Jonathan: antibiotic resistance and synthesis genes
    • This framework could be useful for multiple environments and future grants
    • Call it the "most wanted" list
  • Downstream analyses they can do
    • Genome neighborhood based functional prediction
    • For pathway analysis, start with input (e.g., solute carriers) and try to annotate the rest of the pathway
    • Synthesize/clone proteins
    • Crystal structures
    • In vitro enzyme activity assays
  • Blue Waters: 20 million integer processor hours
  • To do: get list of InterPro with no PFAM (or other annotation)

• Tim Laurent is leaving
  • Get him to document what he did with Sfams several months ago (build 2 families)
  • Ad posted
  • Jonathan will follow up with Katie re: hire and support from his lab on EFI project