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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.
As observed in our previous study with this type of cross-species array platform [15], these data confirmed the trends seen in the microarray data and indicated that the microarray, in general, under-reported the actual levels of changes that occurred across the four time courses.
An artificial data set with four time courses was created.
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sRNA candidates were initially identified using the probe data from the four time course experiments (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).
There were 101 experiments in four time course arrays measuring temperature increase, pH drop, salt increase, and phosphate starvation (Table 1).
The artificial neural network was trained with the data of seven time courses and the other eight time courses were used for testing the network.
Data obtained from seven time courses were used for training of the ANN and another set of data obtained from eight time courses were used for testing of the trained network.
The Hela cell cycle data used in the study [2] consists of five time courses (114 total arrays).
The second drawback of the earlier GLM analysis seems to be that it cannot represent the association between two lagged-time courses due to delayed response, since delayed response implies lack of linear association between two time courses.
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