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The main pathways identified were Glycolysis and Gluconeogenesis, Oxidative Phosphorylation and Proteasome Pathway (Table 3).
While a large proportion of mRNAs within these pairings were unknowns, the main pathways identified were transport, response to stimulus, cell/tissue structure and development and protein synthesis.
29 Partly for this reason, we used generous statistical criteria to identifying plausible pathways for further testing and we also tested some alternative model configurations, which showed that our assumptions about the causal ordering of mediators made little difference to the relative importance of the main pathways identified.
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From our comparison between pristane (arthritis inducer [ 21]) and phytol (NADPH oxidase-activating and arthritis-ameliorating compound [ 20]), two main pathways were identified.
The main metabolic pathway identified for the synthesis of nitrogen into glutamate and glutamine in B. hyodysenteriae involved glutamine synthetase (glnA: BHWA1_00495), glutamate synthetase (gltB: BHWA1_01224) and three copies of oxidoreductase, Fe-S subunit (gltD: BHWA1_00069, BHWA1_00782 and BHWA1_01834).
A tissue-independent development-related minimal essential network derived from this interactome model was associated with the same evolutionarily conserved growth pathways identified in the main data set.
UPR consists of three distinct pathways, identified by their main regulatory factors, namely, the activating transcription factor 6 (Athe), the inositol-requiring enzyme 1 (IRE1), and the double-stranded RNA-activated protein kinase-like ER kinase (PERK) [ 65].
Derived interactome models were associated with the same biological pathways identified using the main data set (Additional file 1: Table S6); 16/19 identical biological pathways in infancy & 9/12 identical biological pathways in late childhood/puberty (as identified by Ingenuity Pathway Analysis [IPA]) (Additional file 1: Tables S5).
The main representative developmental/differentiation-associated (BP) GOs and KEGG pathways identified by the annotation enrichment analysis for all the five clusters are shown in Table 1.
As discussed in the Introduction, there are at least 16 enzymes involved in bile salt synthetic pathways in humans and rodents, with two main pathways (neutral and acidic) identified so far [ 6, 7]. Figure 2 shows a simplified version of the neutral bile salt synthetic pathway.
b Glutamate pathway identified using ingenuity pathway analysis (IPA).
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