Discuss Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging
1. For the statistical test used for differential abundance, it was not stated which of them listed in the Statistical Analysis section was used, but I chose the Mann–Whitney U tests because the median and interquartile range (IQR) with significance were obtained using this test for relative abundance.
2. Prevotella 2, prevotella9 , Coprococcus 3 and Ruminicoccus 2 had no ID on NCBI and Uniprot but on my research, I found out that Using 16S rRNA sequences, Prevotella was reclassified into Prevotella 1-5.
3. Fig4D signatures were curated with respect to the listed significant markers on the figure. Both P-value and FDR were not stated in the paper hence my default threshold was 0.05 I only curated signatures with significant markers of less than <0.05 both for p and FDR which are the purple and green markers.. Signatures with FDR<0.1 were not curated because it seems like that is a weak threshold in statistics to curate for(my opinion)
4. Experiments 4 and 5 were curated as differences between samples eg. Colon vs feces, but it was not stated in the paper which group the samples belonged to, either the control or the case group.. I named group 1 as samples for the case group and group 0 as samples for control.
Also for these experiments, alpha diversity wasn't exactly stated as the experiments was carried out between samples and not general groups.
5. The signature Ruminococcus gnavus group has a different name on the NCBI site called Mediterraeibacter gnavus.
Bacteroidales wasn't curated as it's the order of the genus; bacteroides
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