The samples were biologically evaluated by employing multimode antioxidant, cytotoxic, protein kinase inhibition and antimicrobial assays.
Proteins were isolated separately from tissues dissected from each pool of plants, to produce four paired protein samples from fibres and the non-fibre fraction, where each pair of samples was biologically independent from every other pair.
Firstly, the distinct time-points from the differentiation samples were biologically linked, such that each time point sample from each bio-replicate was derived from a common progenitor (see Figure 1B).
These samples were biologically heterogeneous (outbred population, different aged individuals), heavily premanipulated (overnight enzymatic digestion, frozen, and re-thawed), and fewer cell surface markers are used in the purification of progenitor populations.
These results demonstrate that the radiolabeled biotin in the sample is biologically active and available to cellular enzymes, and specifically labels biotinylated proteins.
Furthermore, the phenotypically anchored genes that were acquired from the prototypes of the clusters from the acetaminophen-exposed samples suggest that the mod k-prototypes algorithm forms groups of samples that are biologically meaningful.
Instead, each is clustered with the fixed samples that are biologically similar: hESCs with fixed hESC cells, and d5 cells+ cells with fixed day 5 samples (Fig. S4).
The observation that sBEFs, PEFs and PSs, identify similarity between samples that are biologically meaningful, indicates that the categorical transformation of the p-values does not affect the observed result, concluding that the observed similarity has a biological meaning rather than resulting from a manipulation of the data.
Our aim was to characterize samples as "outliers" or "non-outliers" in prior-knowledge based pathways, with the hypothesis that, within a pathway, outliers represent samples that are biologically perturbed.
While it is possible that the suspect taxa are genuinely present in these samples, in many cases they are biologically unexpected: for example, rhizosphere-associated bacteria that have been implicated in human disease [ 27, 44].
