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In contrast, the enriched GO terms identified in the fast-evolving genes in the placental marsupial comparison are highly associated with adaptive immunity as suggested by multiple terms associated with T-cells (supplementary tables S2 and S3, Supplementary Material online).
Interestingly, this analysis significantly related the TRIM32-regulated genes to terms, including 'neuron differentiation', 'neuron development'morphogenesissis' and multiple terms associated with neuronal maturation, such as 'transmission of nerve impulse' and 'neuron projection development'.
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In addition, as noted for several genes in the top DMR list, multiple ontology terms associated with cellular metabolism were also enriched for DMR-associated genes (Fig. 4a; Additional file 8: Table S4).
Multiple GO terms associated with both positive and negative regulation of transcription and gene expression (GO 0045935, GO 0045499, GO 0032583, GO 0008634) were also identified due to the inclusion of Fgf23, Myc and Pou2f2 (Additional file 5: Table S5).
By doing so, we are not only overcoming the threshold dependency problem but also using the ranking (true value of the f(N (i, j))) as the confidence scores for multiple GO terms associated with a single protein.
Similarly, several interesting functional GO terms were associated with p-values <0.01 while not reaching the threshold for multiple comparisons included terms associated with lipid metabolism, epithelial and epidermal differentiation and development, cytoskeletal organization, calcium ion binding, and defense response.
We argue that our approach directly addresses evaluation in cases where there are multiple true and predicted (leaf) terms associated with a protein by taking the structure of the ontology and the dependencies between terms induced by a hierarchical ontology into account.
All GO terms associated with a protein were used due to both the multiple associations between GO terms and a given function, and the hierarchical structure of GO terms.
Incorporating multiple species into the analysis significantly improves G omo's ability to identify GO terms associated with the regulatory targets of TFs.
Who wants those terms associated with them?
"I want no mercantile terms associated with me.
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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