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P-values are given for the null hypothesis that the observed ranking resulted from random sampling of the same number of genera from all 88 genera.
Column 5 gives the observed ranking on basis of the transcriptional response towards a glnR knock out mutation (k.o).o
We then use data from the left out strain to predict the expression values of the 50 searched genes for each time point in the this series, rank them according to the predicted levels such that the highest expressed gene obtain rank number one, second highest rank number two, etc., and calculate the Spearman rank correlation with the observed ranking of the same series.
The values in the variables were the observed ranking for the latent variable, y*, of the actual ranking.
The thermostability measures we applied, however, do not correlate with GC-content, indicating that the observed ranking is not influenced by GC-content.
As can be seen in Table 5, large observed ranking intervals are quite possible and can mainly be interpreted as resulting from the limited precision of the instruments.
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Results: The mean observed rank of 5.0 in the Down syndrome group was significantly higher than expected (P ≤.005).
In these cases, the PDMs involved were displayed for the highest common observed rank.
The observed rank correlation coefficients are all significantly lower than those for the random networks (with 95% confidence interval).
Besides the consistency between the predicted and observed ranks, we also studied the performance of the DIGRE model in detecting synergistic or antagonistic combinations.
Although this score estimates the likelihood that a candidate gene would obtain the observed rank by chance, these scores cannot be interpreted as probability values.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com