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sRNA candidates were initially identified using the probe data from the four time course experiments (Table 1).
There were 101 experiments in four time course arrays measuring temperature increase, pH drop, salt increase, and phosphate starvation (Table 1).
The majority of profiles (101/162) were from four time course studies measuring changes in temperature, pH, salt and phosphate concentrations (Table 1).
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There are also a group of 134 genes that are detectably expressed at all times in all four time courses.
The remaining four time courses (and all of the KO, KD and MF datasets) do not provide any information with regard to the targets of a selected perturbation.
An artificial data set with four time courses was created.
Five time course (TC) datasets were provided.
This time series experiment was repeated with the wild type and a soxR deletion strain, resulting in 18 microarray assays from the three time course experiments (two sets for wild type and one set for ΔsoxR).
Therefore, the L/L 4°C time series was not analyzed by transcript profiling, while all four conditions were analyzed by metabolite profiling, yielding a total of seven time course datasets.
Nine time course studies were used for the meta-analysis.
We use eight time course microarray experiments from four previously published works to perform the co-expression analysis [ 14- 17].
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