In MedDRA, this flexibility is artificially limited: Preferred Terms may descend from more than one Higher-level Term, but a given Higher-level Term or Higher-level Group Term may descend from only one SOC.
"Terminal care" is the higher-level term MeSH uses to classify those entries that deal with death and dying.
As a preliminary screening revealed no significance of the interaction terms in any analysis, we performed a type II ANOVA, included in the package car (Fox & Weisberg, 2011), which returns the adjusted sum of squares for the main effects with the higher-level term omitted (Hector, Von Felten, & Schmid, 2010).
Higher-level terms indicated a general trend towards greater organismal complexity, as well as expanded locomotory and sensory abilities characteristic of vertebrates (Additional file 2, Table S2_bp).
The R package annotationDbi [ 55] was used to obtain a full list of associations (along with higher-level terms) from annot8r annotations prior to analysis of GO term overrepresentation in gene sets selected on the basis of dn/ds or expression values.
While its constitution can be completely retrieved in yeast and human based on its GO term (GO 0005885), the same is impossible in P. infestans: the annotation of the encoding genes is limited (only a single member of the Arp2/3 complex has this term) and higher-level terms such as cytoskeleton are too broad and retrieve too many results.
By coarse, we mean that we selected higher-level terms, or those with less specificity, for quality and sometimes entity.
The 3081 GIPC1 KD probesets representing 2271 genes were used in a functional enrichment analysis using Expression Analysis Systematic Explorer EASEE) [25] and nested EASE, which applies the EASE representational analysis iteratively to identify GO daughter terms that drive the significance of higher-level terms (Chittenden et al., submitted).
The ontology matches Internet vernacular to the closest relevant MedDRA preferred term, but allows for less specific higher-level terms to be used when not enough detail is available for matching to a preferred term.
In this study a higher-level Biological Process is defined as any term above the fourth level in the GO Biological Process hierarchy.
