ClueGO Leading group - term with highest significance is not always selected
Jan Söderman
Using ClueGO I have noticed that sometimes it is not the term with the lowest p-value that is selected as leading group term, but instead a term with a higher p-value. I have noticed this behaviour on several occasions in different analysis, and I share one of the analyzed gene lists, and both the corresponding ClueGO log file and a screenshot of the result table. For group 16 the term "ribonucleoside bisphosphate metabolic process" has been selected as leading group term, whereas it is the term "organophosphate metabolic process" that has the lowest p-value. In the analysis I have chosen to show only pathways with pV >= 0.01 (which is not ovbvious from the log file).
Is this a bug or is it more to the selection than just the lowest p-value?
Additionally, if I manually select deselect "ribonucleoside bisphosphate metabolic process" and instead select "organophosphate metabolic process" in the result table this is not reflected in the network ("ribonucleoside bisphosphate metabolic process" is still written with a larger font size) or in the Cluster #1 tab (e.g. the pie chart). How is this labeling updated?
My Cytoscape version is 3.7.1, installed on Red Hat Enterprise Linux Server release 7.6 (Maipo), and the ClueGO version is v2.5.4.
Sincerely,
Jan
Bernhard
Hi Jan,
you are right, generally the term with the lowest p-value is selected as leading group term except for the cases in which groups overlap. In this case, we select the next most significant term. This is the reason for which you see highlighted in the network "ribonucleoside bisphosphate metabolic process". The term "organophosphate metabolic process" is part of four groups, and already highlighted for one of them (light green). Please switch between ClueGO visual styles if the overlap of the groups is not visible on the network.
You can highlight additional terms on the network in the ClueGO+CluePedia panel/ClueGOResults table (the third button from the left side, "Label", will update term names on the network).
Best