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Notably matching the profile of pathways modulated in Vav-deficient macrophages, Themis2 appeared to enhance the LPS-induced activation of both p38 and ERK compared to parental RAW cells whereas activation of JNK in the same cells was unaffected (Fig. 4a, b).
Figure 3 shows the profile of pathways associated with the maximum number of genes in each network.
To understand the stage-wise profile of pathways consisting of Significant DNA methylated genes, these were then annotated with respect to their pathway association using KEGG [ 74, 129].
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Figure 3A shows that the profile of pathway perturbation is indeed informative of chemical toxicity.
Our results demonstrated that the gene expression profiles of pathways effectively distinguished well-characterized clinical types of cancers.
In addition, some disease-relevant pathways or subtype-relevant pathways are well associated with clinical indices according to their DEVGs' relative expression level, which are usually not observed from the raw expression profiles of pathway genes.
Overall, this work represents the first large-scale transcriptome profiling of in vitro tissues for W. somnifera and provides comparative expression profiling of pathway genes involved in withanolide biosynthesis and their potential biological activity.
In addition to relating gene expression profiles of pathway members by their similarity, the data is used to link cause and effect by relating the deleted gene to all transcripts significantly changing in response to the deletion [ 19, 20].
Based on identification of CAGs' catalytic domains, sludge metagenomes recorded a diverse profile of carbohydrate pathways of totally 109 GHs, 16 CEs and 64 CBMs families (Additional file 1: Table S3) comparable to those in animal guts.
These data are in line with the previous observations of an early activation of a similar profile of molecular pathways, following both direct trauma to the spinal cord and sham operation [ 12].
Projection of the gene expression data of the pathway onto the first PC is taken as the expression profile of that pathway.
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