The resulting integrated viral perturbation data reflects rewiring of the host biological networks and highlights pathways, such as Notch signaling and apoptosis, that go wrong in cancer.
The conservation of genes and pathways across species further validates the use of the mouse as a model to study mammary gland development and highlights pathways that are likely to govern cell-fate decisions and differentiation.
Furthermore, poorer survival related to the CHEK2 1100delC gene-expression signature highlights pathways that are likely to have a role in the development of metastatic disease in carriers of the CHEK2 1100delC mutation.
This initial analysis provides insight into the molecular dynamics associated with temporary organelle integration within a host cell and highlights pathways to examine in M. rubrum that might demonstrate compensatory changes or communication between the host and kleptokaryon.
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).
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.
