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We then examined 93 WGA-treated DNA tumor samples for mutations in EGFR pathway genes and a set of exploratory genes (Figure 1).
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The network of miRNAs and target genes was constructed in the software Exploratory Gene Association Networks (EGAN) [ 22].
The Exploratory Gene Association Networks (EGAN) Java desktop application was also used to visualize the interactions among the selected genes [ 38].
A recent exploratory gene-gene interaction analysis of age-related cataract implicated genetic interactions in the genetic etiology of the complex trait [Pendergrass et al., 2013b].
After the introduction of spotted array technology in the mid 90s, microarrays have steadily gained popularity for exploratory gene expression analysis.
To determine the prevalent functional patterns in groups of co-regulated genes, we performed gene enrichment analysis and visualization using GeneMANIA plugin [ 26] for Cytoscape 2.8 and Exploratory Gene Association Networks (EGAN) software [ 27].
Table 2 includes the top five genes with the lowest P-values obtained in the gene-based analysis along with their functions (according to GO annotations).> In our exploratory gene-based analysis none of the genes reached the genomewide significance threshold of α = 4.3 × 10−7.
Exploratory Factor Analysis.
Although these results fail to support prior findings of independent associations of these polymorphisms with smoking status, our exploratory findings suggestive of gene-gene and gene-treatment interactions warrants further investigation.
Exploratory analysis of gene expression and CGH data shows new genes differentiating both subgroups, proliferation associated genes and non-proliferative genes.
For the purpose of exploratory analysis, all genes with a p<0.05 (non-corrected) were considered.
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