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FET p-values had to be transformed to improve interpretation: p-values express a probability, and the smaller they are, the more significant the result is, while from a conceptual point of view it is better to express pathway enrichment as a number that it is either categorical or the more significant the greater it is.
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These results show that moderate pathway expression levels best characterize samples, but the most highly expressed pathway expression scores are also informative.
To this end, efforts are actively underway to develop a high throughput TAR capture method to clone and express pathways in a broad range of host organisms.
After genome editing using this technique, a combinatorial library was obtained with variably expressed pathway genes.
The excretion pathway is the most significant differentially expressed pathway in ccRCC in terms of overall rank, indicating that loss of normal renal function is the most striking biologic alteration.
Scott et al. [12] have also suggested that the fragmented arrangement of Sox genes in T. crunogena could be maintained by the lack of selection pressure for regulation of a constitutively expressed pathway.
Pathway analysis was performed using MetaCore™ (Thomson Reuters, New York, NY) and functional ontology enrichment analysis was performed to find differentially expressed pathway using differentially expressed genes [ 18, 19].
The p53 signaling pathway (pvalue 1.66×10-4) isignificantlyly expressed (the second most highly expressed pathway in the distal colon) in response to AOM.
If a pathway with P-value < 0.05 in a given tissue, this pathway is regarded as expressed pathway in this tissue.
The number of transcripts assigned to this pathway is about 7.5x higher than the second most expressed pathway, 'Photosynthesis' (ko00195), class 'Metabolism'.
The top differentially expressed pathway was Lysosome, which is the cellular organelle involved in the digestion and removal of bacteria (Additional file 3: Table S3).
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