Discuss Diagnosis of Crohn's disease and ulcerative colitis using the microbiome

Experiment 6

This is one extensive study. Experiment 6 was curated from Figure 3J, the taxa identified between HC and UC mild, severe and moderate groups were the same, for both increasing and decreasing signatures. To avoid double entry, I curated them combined. Therefore the sample size for group 1 is Mild=162; Moderate=25; Severe=11

Other experiments

LINDA and Wilcoxon/ T-test were both used to identify significant taxonomic composition. The results which were presented in the Supplemental. Figures S2-S4 could not be curated because there was no clear representation of significance between groups. This was confirmed by my mentor, Chloe during the office hour. However, Supplemental. tables S4, S8 and S9 were curated because significance and direction were both shown.

Selecting a threshold

While selecting a threshold, a more stringent p value of 0.0001 was used to curate the Supplemental tables S2, S5 and S8, to reduce the number of taxa (which was over 200 at p value 0.05/ 0.01)