A total of 10,107 significantly positive differentially expressed (DE) genes were observed from 20,539 genes in the AD microarray dataset based on the two class (disease and control) unpaired t-test, using the false discovery rate (FDR = 0.98).
As one of the data processing steps recommended in [ 13], logarithmic transformation are applied on microarray datasets: base 10 log for data derived from oligonucleotide (Affymetrix) platform and base 2 log for data derived from cDNA (two-color) platform.
Various microarray gene expression datasets based studies have generated gene signatures to predict the prognosis outcomes, while ignoring the large amount of information contained in established clinical markers.
Large-scale integrated microarray datasets typically combine strongly diverging datasets based on different experimental conditions, independent cohorts of samples, varying sample preparation methods and labelling methods or scanner settings, and even different microarrays or microarray platforms.
A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software), can detect underlying global-scale responses, which cannot be detected by means of individual gene expression techniques using raw or corrected p values (FDR).
Using three datasets based on physical interaction assays, genome-wide RNA interference (RNAi) screens and microarray assays, we identified 714 putative DENV-associated mosquito proteins.
Briefly, microarray datasets were grouped based on the cell line.
We used Genevestigator expression datasets (microarray based) to further validate the expression patterns of a subset of those genes expressed more highly in somatic embryos than in leaf tissues by RNA-Seq.
Celsius, the largest co-normalized microarray dataset of Affymetrix based gene expression, was used to calculate the correlation between all possible gene pairs on all platforms, and generate stored indexes in a web searchable format.
Only those TFs identified also for the whole microarray dataset are listed (based on chip-Chip analysis), without consideration of statistical significance.
Relative expression values of PDGF family members were combined with a cDNA microarray dataset and analyzed based on clinical findings and PDGF expression patterns.
