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As already observed by [ 5], many of the known targets of LexA can be correctly identified from microarray experiments present in M3 D since a significant portion of the experiments stored in this database involve DNA damage.
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This interest culminated in human genome-scale microarray experiments presented here.
Microarray experiments presented in this study adhere to the standards proposed by the Microarray Gene Expression Data Society [ 51].
Following completion of the microarray experiments presented here, Hezroni and colleagues [ 40] published data showing limited transcriptional change following treatment of ES cells with VPA.
The P. aeruginosa strains used for the microarray experiments presented in this study were PAO1 (parental strain of the Washington Transposon Mutant Library, [ 12]) and PA14 (obtained from the Ausubel Lab).
Complete results of the DNA microarray experiments are presented in table S2, and the raw data is available from the authors on request.
On this page, the summary and published year of the DNA microarray experiments are presented along with the list of top regulated genes if available.
For microarray experiments, the presented data includes statistical p-values of the significance of biological replicates (experiments performed on different dates), technical replicates (multiple within-experiment replicates), or treatment significance (i.e., Kdo2-lipid A vs. control treatments) on the Select tab of the Node information dialog.
The program GACK was used to convert the data from each microarray experiment to present or absent [49].
Beside the scores of the candidates and the fold-change derived from the microarray experiments, we also present known links to similar diseases with related phenotypes.
The results from microarray experiments are generally presented in the form of an expression data matrix, where rows represent genes and columns represent samples (or vice versa depending on the experimental objective).
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