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The MAQC set is an excellent proxy problem for a real-world microarray experiment in which researchers would predict transcript concentrations based on a spike-in calibration mixture.
Every microarray experiment in the collected publications generates lists of genes that are found to be characteristic of some condition or timepoint (see [22]).
In this table, "Condi" refers to one microarray experiment in the ith condition (not necessarily all the conditions have to be different).
There is no clearly "correct" method for taking what is learned by microarray experiment in culture and applying it to assess pathway activity in tissue samples.
In the few cases where it was not possible to extract the control cell line values from the experiment (mir-1 Lim et al. [5] and mir-124 Lim et al. [5]), filtering genes from the negative controls from a microarray experiment in the same cell line were used (mir-98 negative controls Gennarino et al. [53]).
A typical microarray experiment in our laboratory involves handling 5 or 6 microarrays in a batch.
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We performed DNA microarray experiments in order to compare gene expression responses to the heat treatment at 39°C with the gene expressions in non-treated control cells.
Use of rationally designed microarray experiments in IFN biology yielded informative clusters that may provide candidate genes for diagnostic or for evaluation of therapeutic possibilities.
All microarray experiments in this study are available from the TAIR database (https://www.arabidopsis.org/servlets/Search?type=expr&search_action=new_search) (Submission Number(s): ME00325, ME00338, ME00328, and ME00339).
We also performed microarray experiments in PC12 cells to gain insight into the molecular changes that may mediate this phenotype.
In contrast, whole genome microarray experiments in synthetic complete (SC) medium reported that Mediator associates with many genes at both promoter and coding regions.
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