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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.
After genome editing using this technique, a combinatorial library was obtained with variably expressed pathway genes.
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.
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.
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).
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.
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An edgeR-based differential expression analysis showed 20 differentially expressed pathways in total among paper, CS and SR-fed termite guts at FDR False Discovery Ratee) < 0.05 (Table 2).
Enrichment analysis was performed on significant genes to identify differentially expressed pathways.By comparing the gene expression profile of keratinocytes from E16 versus E18 fetuses, we identified 24 genes that were downregulated at E16. Analysis of E16 and E18 fibroblasts revealed 522 differentially expressed genes.
Our problem is to choose an error control procedure to determine a P-value threshold for identifying differentially expressed pathways in high-throughput gene expression studies.
Thereafter the pathway-level aggregated expression data, or simply, pathway expression data, are directly analyzed to identify differentially expressed pathways.
This method uses a factor graph model combining gene copy number variation data with gene expression data for the identification of differentially expressed pathways.
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