Moore Notes 8 13 14
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TJS taking notes in KP's stead
Participants: TJS, PB, SN, SW, DW, SH
Topics for discussion
- Patrick's presentation
- analyzed metahit cohort with shotmap (N=39)
- annotated into MetaCyc, SFam, KO
- have BMI, IBD, gender, age covariates
- corrected for AGS using MicrobeCensus
- conducted rank-based tests of correlation (wilcox & kendall)
- multiple tests corrected with q-value
- using q<= 0.25, ibd-3 (none v. CD v UC) is only covariate with any real differentiation
- Sfams have relative few sig hits
- There are 429k families in at least 1 sample. Multiple test correction a problem
- Was one (or more) of the samples processed with round 2?
- analyzed metahit cohort with shotmap (N=39)
- Can we filter families that we are testing to improve discovery
- considered various family properties that is independent of the test statistic
- as we filtering by mean, we do see some gain in discovery, though in SFams requires throwing out lots of data
- variance filtering has similar pattern as mean, as expected
- filtering for fraction 0 only impacts ibd-3 and is generally helpful
- Q: how does number of samples impact these results
- Q: can you label the cutoffs on the final image?
- Q: Sfams lots of families are eliminated; could be the round 2 and the poor recall families (which are usually low abundance) that SN identified through simulation
- Observation: This is a lot like the pipeline optimization, but at the test statistic level. Should fit into narrative nicely
- Coefficient of Variation has inconsistent results
- SFams ibd3 has a result we don't trust. Not exactly sure what's happening here
- filtering does seem to help with ibd3, biggest gains for SFams. Fraction observed helps all 3 and can use a single, strict cutoff for all databases (85%).
- considered various family properties that is independent of the test statistic
- Can we filter families that we are testing to improve discovery
- pathway enrichment (Fisher's exact test)
- Used q-family < 0.25 and q-pathway of 0.25 or 0.1
- has done kegg and metacyc, for sfams will need interpro2go
- found more modules higher in CD than lower
- Slide 21 has some interesting examples
- LPS. Let's check to make sure this is real.
- cobalamin (B12) biosynthesis showing up in both KO than MC
- Oddly, short chain fatty acid biosynthesis elevated in CD. What is going on here?
- Slide 21 has some interesting examples
- Lower in CD
- All three domain ribosomes, a little worrisome given that AGS correction should take care of this
- What is AGS by disease state distribution? What is abundance of ribosome before and after disease state.
- Also, why is sulfate lower? Morgan et al showed higher in IBD. Do see some similarities
- All three domain ribosomes, a little worrisome given that AGS correction should take care of this
- pathway enrichment (Fisher's exact test)
- PCA on gene family abundances
- differentiation does seem to exist in KO for CD v. rest in PC2, PC3, but generally little distinction
- Might need to drop UC-21 which appears to be outlier (and has low seq quality)
- Can we recapitulate what they did with taxonomy?
- Used metaplan, but don't see the same separation.
- May need to contact the authors to see what's going on.
- PCA on gene family abundances
Next week's call:
- Josh & Tom
- MetaCenter meeting update?