If a node has multiple Molecular Function annotations, the most specific annotation will determine the node color.
Nevertheless, GDH identifies a specific node at most and the minimum is 1.
For instance, the Tdh1p-2p-3p isoriginatehich originathreeree FN with identical protein contents, are merged into one FN that retains the two most specific labels (glycolysis and gluconeogenesis; node 6094 + 6096), while the most generic term (glucose metabolic process; GO 0006006) is excluded.
These nodes contain the most specific and informative annotations that resulted significantly enriched.
To reduce the term correlation, we use only the most specific terms, i.e. the leaf node term after propagating the scores of the non-leaf terms down to the leaf node terms.
Moreover, we use the most specific functional terms, i.e. the leaf node terms, to minimize the inter-correlations between terms.
Ideally, each protein should be annotated with a GO term on a leaf node, in other words, with the most specific annotation.
When a user clicks a specific node in a pathway, she/he is most likely to be not interested in the gene, protein, enzyme, etc. in general that the node represents.
The aim of this study was to analyze the relationship between the primary mammary tumor and its lymph node metastasis based on immunohistochemical molecular characterization to develop the most specific prognostic-predictive models and targeted therapeutic options.
In this case, the nodes are merged into one FN, and only the most specific term (i.e., the one with the greatest distance from the GO root) is retained as label.
