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Our analysis showed the three most significantly represented pathways to be acute phase response, followed by actin cytoskeleton signaling and tight junction signaling (Figure 2).
Cardiovascular System Development and Function emerged as the most significantly represented physiological category enriched within the NP transcriptome, independent of expression trend.
The IPA network called "antigen presentation, inflammatory response, cell-to-cell signaling and interaction" was the most significantly represented by the list of dissimilar genes.
(XLSX 9 kb) Additional file 6: In this file we provide the list of most significantly represented pathways among NEUROD2 target genes (http://david.abcc.ncifcrf.gov/home.jsp).jsp
Protein lists were uploaded with Ensembl mouse accession numbers and core analysis was performed to identify the biological functions most significantly represented in the dataset.
The most significantly represented ontology classes were connected with neuronal cells building proteins, adhesion molecules, cell junctions, and hormone and neuropeptides activity (Table 2).
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Among the down-regulated genes, one oncogenic pathway emerged as the most significantly over represented, the Wnt/β-catenin signalling (p<0.001).
Functional gene ontology (GO) annotation analysis revealed that one of the most significantly over represented gene families in the invasive tumor stroma was annotated to the term endopeptidase activity and contained transcripts encoding proteolytic enzymes, including lysosomal proteases, asparaginyl endopeptidases, matrix metalloproteinases and proprotein convertases (Table S2).
Within these biological processes, the most significantly over represented term was oxidation-reduction process (GO 0055114, 92 genes within this term).
The three most significantly over represented terms were regulation of biological quality (GO 0065008), response to biotic stimulus (GOO 0009607) and ion transport (GO 0006811).
We also identified oxidative phosphorylation as the most prominent metabolic pathway significantly represented only in cumulus cells, but not in oocyte suggesting a hypothesis that cumulus cells may also provide energy to oocytes in the form of ATP.
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