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Three methods were discussed in the paper: one focusing on pathways determined enriched in a given experiment, another looks at both enriched and non-enriched pathways, but using only the experiment's resultant genes, and the final grouping the pathways in a de novo, experiment independent manner.
Conceptually, it is likely that because the pathway is the underlying unit of the phenotype, focusing on pathways increases signal and reduces noise.
Focusing on pathways showing a high fraction of disease-associated proteins, we found no correlation of microRNA target enrichment and the fraction of disease-affected signaling proteins (see Figure S3).
We went on to explore the role of individual reactivated genes and their protein products in Aza responsiveness, focusing on pathways known to induce growth arrest and/or apoptosis, and further examination of known Aza effects other then DNA demethylation.
We have attempted to minimize these limitations by employing rigorous statistical techniques, focusing on pathways as much as on individual genes, using protein interaction data to corroborate co-expression findings and using selected protein measurements, including previously implicated post-translational modifications.
These results are intriguing and suggest that future research focusing on pathways driving Akt signaling is warranted.
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The main aim of this study was to analyze the gene profile of human pleural mesothelioma versus normal parietal and visceral pleural tissues, focusing on pathway analysis and differential gene expression correlated to gene function.
Integrating the genetic enhancement results for these 107 genes provides a framework for future studies focusing on pathway interactions in the maintenance of cell-cycle quiescence.
Firstly, the analysis focusing on pathway maps highlighted a number of pathways significantly represented within the gene list, with the transforming growth factor (TGF-β) signalling pathway being most over-represented within the list (Table 4).
NICOLE TORRES: So I do want to talk about the third principle, which focuses on pathways.
This paper focuses on pathways related to the Gal1 gene, which is highly researched for characterizing as a model to understand how gene expression is induced and repressed.
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