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The 104 microarray experiments (corresponding to the three time points of the 28 septic shock and the 25 healthy volunteers) were performed as previously described [18].
By integrating expression data from a compendium of 437 microarray experiments corresponding to 75 different drugs and culture conditions [ 77], we correctly predicted 6 of 7 known inhibitors within this data set [ 46].
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However, this hypothesis relied on a single microarray experiment corresponding to only two time points in late S-phase.
Genes were considered to be expressed, if significant expression was observed in microarray experiments, or corresponding proteins were found in proteome analyses.
Bayesian modeling was performed by using a clever modeling approach that considers three elements in a signaling pathway: a set of transcription complexes, a set fo target genes and a set of transcripts (from microarray gene expression experiments) corresponding to the target genes.
The integrated differential gene expression toolkits delivered similar results as corresponding microarray experiments (data not shown).
For the same RNA-seq data, corresponding microarray experiments were conducted by MAQC with Affymetrix Human Genome U133 Plus 2.0 arrays (GEO: GSE5350).
In order to give biological annotation to REGs, we decided to utilize microarray data to predict the biological responses of cis-elements that are defined by the corresponding microarray experiments.
The -fold inductions of expression generally were higher in the qPCR assays than in the corresponding microarray experiments, reflecting the different sensitivities of both methods (see additional file 5: correlation plot of all data points).
For each sample for which CNV calls from SNP microarrays were available, stringent CNVs detected using the Agilent 1M array were overlapped with the stringent CNVs detected by corresponding SNP microarray experiments (Marshall et al. 2008; Pinto et al. 2010; A.C. Lionel, unpublished data).
20 With differentially activated TFs obtained under the given conditions, we applied our ACTPATH algorithm to identify STP segments corresponding to the activated TFs in the microarray experiments.
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