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All sequence datasets, alignments, spreadsheets, annotation files, output files and lists of gene ontology terms for analysis are available at the Dryad link associated with this study.
As top-level GO terms tend to be annotated to many proteins and leaf-level GO terms to very few proteins, in order to avoid bias in our analysis, we keep only "informative" GO terms for analysis.
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Term-for-Term analysis represents the standard method of performing statistical analysis for over-representation in GO.
Significance of enrichment within arCOG categories was calculated using term-for-term analysis as described [ 49].
As parameter settings, term-for-term analysis with Benjamini-Hochberg correction was used.
In addition we selected genes significantly affected by CsA in WT-PCLS and FXRKO-PCLS identified in the significant GO terms for further analysis by hierarchical cluster analysis (HCA) and functional clustering (see below).
This article suggests some basic terms for surveillance analysis.
Therefore, we only use informative CC terms for our analysis.
However, as the Gene Ontology is hierarchical, we only use informative CC terms for our analysis.
We used GO molecular function terms for consistency analysis as described in Section 2.2.
Learning outcomes for this packet included the interpretation of statistical test results and knowledge of important terms for data analysis.
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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