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This work minimizes cost-constraining variables by mapping the battery design space with the techno-economic model, through which we highlight pathways towards low price and moderate concentration.
This protocol allowed us to highlight pathways implicated in the analysed phenotypes which would not be identified by considering only predicted targets, hence giving further insight into the mechanism of expression of the observed phenotype.
A gene set test (GST), implemented via the Limma package [19], was used to highlight pathways that are differentially expressed as a set, for all genes ranked via P values, and adjusted by false discovery rate (FDR).
The core of our investigation was, therefore, not only to highlight pathways for which activity is selectively modulated by words and pseudowords, but also to expand upon previous reports by locating those that are liable to predict reading performance.
IPA was used to highlight pathways and diseases which involve secreted proteins.
The PM can also highlight pathways linked to a pathogen's virulence.
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To simplify overall interpretation, we only reported "upregulated" categories to highlight pathway activations caused by the disease rather than pathway inhibitions.
Figure 5 and additional file 6 demonstrate the use of the "import class-set" function to highlight pathway components regulated in response to a timecourse of Ifn-β treatment of mouse bone marrow derived macrophages (GEO accession GSE20403).
Highlighting pathways according to experimental data provides some clues on metabolic processes.
Almost all of these genes encode immunoregulatory proteins, together highlighting pathways by which melanocytes might be recognized and killed.
This Figure outlines the routes of metabolism for glucose, alanine and glutamine, highlighting pathways and metabolites in common.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com