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We then identified stemness-on and –off modules using recurrence, cell-diversity, and specificity applied to the remaining 80% of the gene lists.
Values near zero indicate either that an experiment's queries have little overlap with any stemness-on or –off modules, or that they overlap with modules from both in equal proportions.
To identify functional themes, we next clustered all of the stemness-on and –off modules detected by S-MAP according to their patterns across the expression compendium (Figure 5A).
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One-off modules allow students a chance to study anything, negotiated with a tutor.
Last week the vice-chancellor, Professor Bill Ritchie, circulated a memo to heads of departments at the university saying that, due to understaffing, he intends to cancel admissions to the Independent Studies department for undergraduates and for one-off modules.
The stemness-off modules were composed of 39 homolog and 23 functional modules each representing putative programs requiring active repression for the maintenance of stemness (Dataset S1).
Strikingly, of the 350 modules with significant recurrence, 162 stemness-on and 62 stemness-off modules had significant cell-diversity and specificity scores (Figure 3).
A positive SI indicates that the experiment's positive gene list has higher correspondence with stemness-on compared to stemness-off modules relative to the experiment's own negative gene list.
We first computed a stemness enrichment score (SE) to measure the difference in the average overlap of a set of up-regulated genes to stemness-on compared to stemness-off modules (see Methods).
Reprogramming candidates essential for stem cell properties are likely found among the stemness-on modules while stemness-off modules likely contain genes that have to be silent in stem cells.
We used the set of stemness-on modules M+ and stemness-off modules M− identified by S-MAP to develop a score capable of recognizing that a new query set of differentially expressed genes Q is enriched for stemness modules.
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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