In addition, we developed a new software to analyze the microarray data, focusing on how specific transcriptome changes may be associated with enhanced biofilms accumulation, survival and virulence of this pathogen.
Given the importance of these legume natural products [ 79, 80], we examined our microarray data focusing on the flavonoid pathway.
To define the biochemical pathways regulated by ATRA and potentially involved in the anti-tumor action of the retinoid, we performed gene-network enrichment analysis of the microarray data, focusing on Luminal/ER+ tumors.
When we re-analyzed the microarray data focusing our analysis only on the list of these 66 previously published β-catenin target genes, we identified 21 (DLD1), 30 (SW480), and 34 (LS174T) of these genes as differentially regulated in the three cell lines, respectively.
Many of the current approaches for identifying relevant genes associated with survival phenotypes using microarray data focus on trimming or extending a Cox regression model [ 7], a commonly used model of analyzing survival data in traditional clinical settings.
Upon thorough functional analysis of microarray and ultrasequencing data focused on the 6 h time point, we were able to detect cell death, cell growth and proliferation, cellular movement and development responses to EGF stimulation.
Since the Wnt pathway is known to be involved in neural stem cell-differentiation in contra-acting ways (i.e., maintain stemness versus inducing differentiation [19] [21], the investigation of the microarray data was focused on Wnt pathway-related gene sets.
Microarray data was focused on the Affymetrix platform in order to reduce variance arising from platform inconsistencies.
Previous analyses of systematic errors in microarray data have focused on problems at the level of sample preparation, labelling, or hybridization.
Details of this analysis are listed in Table 4 and illustrated graphically in Figure 2 and Figure 3. Conventional analysis of microarray data remains focused on the detection of differentially expressed genes or gene sets.
