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Co-expression interactions are calculated from the MegaYeast expression dataset (Gasch, 2012), which contains 501 yeast microarray experiments measuring expression during stress responses, sporulation and different cell cycle phases.
In 2009, Dudley et al. [ 23] evaluated 429 experiments, representing 238 diseases and 122 tissues from 8435 microarrays, and found evidences of a general, pathophysiological concordance between microarray experiments measuring the same disease in different tissues.
We demonstrate our method on simulated data and a set of time-series microarray experiments measuring the effect of a drug perturbation on gene expression levels, and show that it outperforms leading regression-based methods in the literature.
Further work is possible to study later stages, apply other methodologies to study gene expression, and to compare to other microarray experiments measuring stem cell gene expression changes with differentiation.
The data includes a compendium of microarray experiments measuring the expression levels of 4511 E. coli genes (344 of which are known transcription factors) under 805 different experimental conditions.
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The most important feature for identifying known targets of Swi6 is a microarray experiment measuring expression of genes in an Mbp1 deletion mutant.
Another level of noise originates from the fact that each microarray experiment measures a single value for a gene that reflects its activity averaged across many biological processes.
In brief, this microarray experiment measured changes in gene expression patterns in three different types of cassava roots, including fibrous, developing storage and mature storage roots which are believed to possess distinct predominant metabolism, especially those related to starch biosynthesis.
As microarray experiments measure the steady-state levels of mRNA and Spt5 is involved in many aspects of mRNA stability by virtue of its association with many components of the transcriptional machinery, many of the genes differentially expressed in fogsk8 mutants might represent mRNA processing targets of Spt5.
Typical microarray experiments measure the concentration of thousands of mRNAs simultaneously.
Conventional DNA microarray experiments measure transcript levels of mRNA molecules in arbitrary units, and hence any kinetic parameters in a fitted model result in unit free as well as quantities of regulatory proteins.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com