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Through this DBN computational approach, the method identified significantly perturbed pathways and GO category groups of genes that define the pathogenicity signatures of the infectious agent.
The FA-correlation method identified significantly more FA in the second digit (the index finger) in males with non-affective psychosis compared to normal controls (p = 0.02), and when comparing non-affective psychosis with affective psychosis (p < 0.001) (Table 2).
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This method identifies significantly enriched gene sets by testing two related null hypotheses: 1) The pattern of expression for the genes in a particular gene set is the same as all the other genes, and 2) the gene set does not contain genes with expression profiles that are correlated with treatment.
In addition, the bayesian method identified a significantly higher proportion of eyes with progression by optic disc stereophotographs compared with the OLS method (74% vs. 37%; P = 0.001).A bayesian hierarchical modeling approach for combining functional and structural tests performed significantly better than the OLS method for detection of glaucoma progression.
In contrast, the per-gene regression method identified fewer significantly differentially expressed genes and the p values were larger than those from the other two methods.
Conesa, A., Nueda, M. J., Ferrer, A. & Talon, M. maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments.
Further analysis of survival among different developmental stages identified significantly greater survival of T. noae between the pediveliger and juvenile development stages with the extensive culture method.
The fast implementation also makes it possible to use new clustering strategies, and we describe two methods that identify significantly higher quality models than the widely used Spicker (Zhang and Skolnick, 2004) and the recently published Clusco (Jamroz and Kolinski, 2013) packages.
The local Getis-Ord Gi* method identified eight FSAs with significantly high SIRs and one FSA with a significantly low SIR. The Local Moran's I method detected five FSAs with significantly high-high SIRs, one FSA with a significantly low-low SIR, and four significant outlier FSAs (one high-low, and three low-high).
To further test this hypothesis, we used the previously described "gene module map method" [24] to identify significantly enriched cytobands in the AE microarray data set.
Using the "gene module map method" [24] to identify significantly enriched Gene Ontology (GO) terms [25], we found that "immune response" was the most significantly enriched GO term in up-regulated AE genes (P<10−73) and "lipid metabolism" was the most significantly enriched GO term in down-regulated AE genes (P<10−33) (full list of enriched GO terms is provided in Supplementary Table S2).
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