These were representative genes identified by pathway analysis to be involved in angiogenesis, signaling (wnt, integrin, cadherin, JAK/STAT, Notch, VEGF pathways), cell cycle, apoptosis, inflammation, oxidative stress and developmental pathways (Table 1).
In this study, we determined the 11 most significantly enriched pathways with differentially expressed genes identified on microarray analysis by KEGG pathway analysis to explore their functional role.
This transcriptome analysis was further enhanced by a pathway analysis to understand the pathways that might be disturbed in the two rice plants carrying Xa21.
We next set out to identify the canonical signaling pathways that possibly underlie tumor cell responses to arsenic trioxide by applying pathway analysis to the 209 differentially expressed genes (see Methods).
For instance, one algorithm called PHIAL applies a heuristic method to rank alterations by clinical and biological relevance, followed by intra-sample pathway analysis to determine potentially druggable nodes [ 22, 37].
By applying KEGG pathway analysis to the 6124 probes differentially expressed in PIK3CA-mutated tumors, we identified physiological pathways directly or indirectly associated with PIK3CA mutations.
We therefore searched for alternative n-3 LCPUFA-responsive genes and biological pathways by applying Pathvisio pathway analysis to our transcriptome data sets.
We next compared the Notch pathway between the three sensitive (CRC040, 021, and 001) and three most resistant explants (CRC020, 007, and 034) by gene array and KEGG pathway analysis to determine if tumours sensitive to PF-03084014 had elevated levels of the Notch pathway.
However, the relevance of CXCL11, TNFSF13B, TNFRSF9, and other NF-κB interacting proteins recognized by pathway analysis, needs to be further investigated in relation to diagnosis and monitoring of CD.
However, the diagnostic relevance of CXCL11, TNFSF13B, TNFRSF9, and other NF-κB interacting proteins recognized by pathway analysis needs to be further investigated.
The integrated overview of the various aforementioned genes that is provided by pathway analysis tends to support the notion that genotoxic stress has activated p53 and Gadd45 signaling, two pathways associated with DNA damage [ 79, 80].
