Regarding the pcc metric, all algorithms showed high average values, indicating a good degree of correlation. However, it is interesting to note that prosampler had the lowest minimum value (0.600) in this metric. Such a minimum value is significantly lower than the others, which may indicate ...
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To define the adjacency matrix, the similarity of OTU abundance across all samples should be measured first. Such similarity measures the degree of concordance between the abundance profiles of OTUs across different samples. Similar to widely used gene co-expression analyses [20,61,85,86], Pairwis...
As before, colours and asterisks indicate the degree and significance of the correlation. Statistical significance is indicated by asterisks in the group comparison graph (B) and the correlation heat map (CD). No asterisk represents P ≥ 0.05, indicating no statistical significance. An asterisk...
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The closer to red, the higher the Degree score. (B) The PPI network of the hub genes and interacting genes. Disconnected nodes had been hidden in the network. The ROC curves of (C) PTGS2, (D) LRRK2, (E) ANXA5, (F) IGF1R, (G) MCL1, (H) TIMP2, (I) LYN, (J) CD68, (...
The dataset used in our experiments comes from O-GlycBase, a resource containing experimentally verified glycosylation sites compiled from protein databases and literature. The dataset is available online [16]. O-GlycBase v6.00 [35] contains no identical protein sequences, unless there are conflicts...
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In order to obtain a direct quantitative measure for the degree of AM-related conservation, we defined the conservation ratio, which represents the ratio of the averaged E-values from psiblast (as log10) between the non-mycorrhizal species, and the AM-competent species (dicots or monocots, res...