Three publicly available mouse microarray datasets were included in this study, corresponding to 51 arrays.
Four mouse microarray datasets totaling 141 arrays were obtained from ArrayExpress for further analysis (Table 1).
Underlying GeneFriends is a genome-wide co-expression map created using over 1,000 mouse microarray datasets.
We have created an online tool, called GeneFriends, which identifies co-expressed genes in over 1,000 mouse microarray datasets.
For example, a gene considered SP must also satisfy the MS condition, but we labeled it as SP. We considered five datasets (including the four mouse microarray datasets and the UniGene EST dataset) as five voters.
Our study is based on the Affymetrix ATH1 Genome Array platform here, but our approach can be transferred to any platform, organisms and experimental design which allows one to compute a logarithmic fold change, e.g. human or mouse microarray datasets.
As noted in our previous meta-analysis of large mouse microarray datasets [ 19], the maturity of cDNA microarray technologies has made it possible to compare profiles based upon their biology and not according to the laboratory that generated them, a particular problem in the early days of microarray analyses [ 51].
The model again showed a substantial capacity to distinguish between MI and control samples (tested on independent mice microarray dataset, AUC = 0.86, P < 0.0065 vs. random model, Figure 5).
We then examined the relationship between H4K5ac and gene transcription using a publicly available whole mouse genome microarray dataset (Agilent) for gene expression immediately after CFC in the mouse hippocampus [ 4].
The human and mouse OPMD microarray datasets are publicly available at GEO repository under the accession numbers GSE26605 and GSE26604, respectively and have been previously published [ 14, 15].
