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Although microarray data based on analysis of end-point PCR amplicons is not quantitative, results showed a significant signal reduction when targeting killed cells and consistently agreed with qPCR results.
These genes were selected from the microarray data based on i) their minimal variability between the control and infection group ii) their absolute expression level covering the whole array signal range.
The microarray data based on signals from polyadenylated chloroplast transcripts also indicated that PSII genes like psbE, psbH, psbY and psbX were down-regulated as a response to the HL treatment during some or all of the acclimation phases.
There is not a strong consensus among the three gene sets we used [23], [24], [26], with about 13% (69/513) overlap, There are 67 genes in common between the two microarray experiments and two between the ChIP [26] and the McElwee et al. [23] microarray data, based on our filtering criteria.
We used different methods to analysis the microarray data based on different hypotheses.
256 genes were selected from the microarray data based on association with smoking or coronary artery disease (CAD).
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HUR RNA: Human Universal Reference RNA mAdb: microarray data base The author(s) declare that they have no competing interests.
All these 40 down-regulated genes were found to be up-regulated in various cancer tissues as shown in the Oncomine microarray data base (27).
We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways.
The data sets generated based on the preparations of total RNA following the methods A and B have greater average statistical power than the microarray data set based on method C [see Additional File 1, Supplementary Figure 4].
For example, most classification and regression methods for microarray data are based on the whole set of genes and have not made use of pathway information.
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