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The hits of motif 1 screening within ORFs are shown in Additional File 2. Seven of them could have functional relevance to the ato system based on their GOT analysis.
As predicted by the GOT analysis, many of the targets are transcription factors, transporters and enzymes effecting cellular redox state (Table 5).
The GOT analysis, as implemented in this work, evaluates whether the information content captured by a motif implies random noise or is a biologically relevant one.
Results of the GOT analysis of motifs 1, 2, 3 and 4, at prior probability set to 0.7 (corrected p-value cut-off set to 0.1).
In order to overcome this limitation and test the discovery strengths of the proposed analytic pipeline in this work, we applied this to motifs that score lower during the Motif Sampling phase (assuming that they reveal weak matching with the atoDAEB promoter binding site) and examined them separately regarding their evaluation in the GOT analysis.
Cluster-based GOT analysis connected regulated genes in each cluster to several functional categories where regulated genes are overrepresented.
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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