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As shown in Figure 5, unsupervised hierarchical clustering of the oncogenic pathways E2F, PI3K, Myc, β-catenin, Src, and Ras in the cohort of 133 patients demonstrated significant, biologically relevant patterns of pathway activation.
However, although theoretically possible, we could not detect biologically relevant patterns of anticorrelation, in line with previous studies [ 14].
Using DNA methylation, gene expression and microRNA expression data of ovarian cancer samples, he showed that the method is able to uncover biologically relevant patterns of complex gene regulatory systems.
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Moreover, there is no clear method of distinguishing biologically relevant patterns attributable to distinct risk factors from sporadic patterns due to noise.
Our approach serves as a way to extract biologically relevant patterns from large, heterogeneous, omic datasets in support of subsequent, hypothesis-driven experimental studies.
To leverage the microbiome community for the benefit of human health, analysis approaches will have to explore more than just the community structures of microbiomes to find biologically relevant patterns.
We investigated the relationship between promoter region TR allele length (NAL; Table S2) and gene expression (RPKM; Table S3) both by species and combined, using a series of regression models chosen to represent biologically relevant patterns.
The resulting data were then analyzed by using sophisticated software and statistical methods to identify biologically relevant patterns.
Opening these large data sources to the community, or at least within collaborative networks, will facilitate the comparison of results to detect and correct issues with the methods, identify biologically relevant patterns or anomalies, and provide insight for new experiments.
Because of the exploratory purpose of this analysis, we set alpha = 0.10 for all comparisons to better detect biologically relevant patterns in head size [48].
We therefore developed statistically valid, novel approaches to data analysis that can identify biologically relevant patterns in a noisy dataset.
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