Sentence examples for modules were performed using from inspiring English sources

Functional enrichment analyses of these 525 modules were performed using terms from the GO biological process and KEGG pathway (Tables S5 and S6).

The test to calculate the average delay of LibrasTV modules was performed using a real DTV signal as input during a whole day (24 h).

Gene set enrichment analysis for PrCa-associated modules was performed using the hypergeometric test.

Functional examination of the genes represented in these two modules was performed using Ingenuity (Ingenuity® Systems, http://www.ingenuity.com).com

Realignment around indels, Q-score recalibration (using SNPs from [ 10]), and variant (SNP/indel) calling by the UnifiedGenotyper module were performed using GATK (v. 1.4-37 1.4-37 46].

Venn diagrams were drawn using Venny (http://bioinfogp.cnb.csic.es/tools/venny/) and statistical analysis of genes that were categorised in the PRC module against those in either the Myc module or the Core module was performed using the Chi-square test.

Firstly, GO enrichment and GO clustering of the genes within each module was performed using DAVID [ 4].

In addition, ontological analysis of each identified module was performed using GOstat [ 45], to examine the biological themes and the functional relationship of the module members.

For all survival analyses, patients were dichotomized on module expression above or below the module average and survival analyses were performed using the survival package in R. To control for dataset bias in survival analysis in the U133A set, robustness of results was evaluated in a leave-one-out analysis excluding one dataset at the time (data not shown).

To predict functions of the expression modules, the GO enrichment tests were performed using the hypergeometric distribution [19].

Partial correlation analyses were performed using modules of the "ppcor" package (v.1.0) [ 41] for R (http://www.r-project.org/).org/