Heatmap visualizations of microarray data were created in R using the heatmap.plus package (with slight modifications to make more compact dendrograms) and the marray package to create the green to red colour scheme.
Using publicly available T. gondii expression microarray data, we created Toxoplasma gene sets related to bradyzoite differentiation, oocyst sporulation, and the cell cycle.
In terms of different study, the methylation microarray data were created in different times, places, and by different technicians and so on; therefore, the main variation among data would be shown as a batch effect.
To test whether Fkh TFs regulate the Ndg enhancer, we used relevant protein binding microarray data to create a series of Fkh-binding site mutations in the wild-type sequence (Fig. 1B; supplementary material Table S1).
In recent years, wealth of expression data emerged and several online repositories for microarray data have been created, including NASCArrays [ 8], Genevestigator [ 9], PLEXdb [ 10], MetaOmGraph [ 11], ArrayExpress [ 12], Vanted [ 13], Virtual Plant [ 14], ATTED-II [ 15], Arabidopsis Coexpression Data Mining Tool [ 16], MapMan [ 17], and PageMan [ 18].
However, one intractable problem with using microarray data analysis to create cancer classifiers is how to reduce the exceedingly high-dimensional gene expression data, which contain a large amount of noise.
Thousands of microarray data repositories have been created for gene expression investigation [1]; sophisticated cameras are becoming ubiquitous, generating a huge amount of visual data for surveillance; the Square Kilometre Array Telescope is being built for astrophysics research and is expected to generate several petabytes of astronoimcal data every year [2].
Inferring Gene Regulatory Networks (GRNs) from time course microarray data suffers from the dimensionality problem created by the short length of available time series compared to the large number of genes in the network.
The graphs were created using Rembrandt microarray data for the probes from the Affymetrix U133 Plus 2.0 GeneChip and associated survival data.
