From these data, we selected 12 microarray datasets corresponding to rice plants treated with chilling (10°C, 3 time points), 25% polyethylene glycol (PEG) 600 (simulated drought stress, 3 time points), 260 mM mannitol (stimulated osmotic stress, one time point), 150 mM NaCl (one time point), submergence (3 time points), and 0.2 ppm ozone (one time point).
To assess the performance of our statistical tests, a human Affymetrix microarray dataset corresponding to 47 subjects with acute lymphoblastic leukaemia (ALL) and 25 subjects with acute myeloid leukaemia (AML), as previously described by Golub and colleagues [5], was downloaded from: http://wwwmaths.anu.edu.au/johnm/r/hddplot/.anu.edu.au/johnm/r/hddplot/
It can sample from these transcriptional regulatory networks, and produce corresponding microarray datasets parameterized by the network topology, size of the network/number of genes, and type of experimental noise etc. Network topologies are generated by selecting sub-networks from a previously described Ecoli network.
Three publicly available mouse microarray datasets were included in this study, corresponding to 51 arrays.
In order to test the relationship between gene connectivity within the co-expression network and gene essentiality, we first constructed three networks corresponding to three microarray datasets.
We investigated the regulation of signaling networks with twenty microarray datasets from eleven different tumor types and their corresponding non-malignant tissue samples.
Three microarray datasets are used to test the ensemble systems, and the corresponding results demonstrate that these ensemble schemes can further improve the performance of the ICA based classification model, and the third fusion scheme leads to the most accurate ensemble system with the smallest ensemble size.
Applying our methods on several microarray datasets, we have discovered many significantly activated TFs and their corresponding pathway segments, which are supported by evidence in the literature.
The web server can lead the user to datasets corresponding to specific tissues, conditions via identifiers of the microarray studies or hybridizations, keywords, official gene symbols or reference transcript identifiers.
This enrichment was further validated in the independent microarray datasets (Supplementary Fig. 25).
A scalable method for integration and functional analysis of multiple microarray datasets.
