Among the genes assayed by qPCR, those that were labeled as "signature" (genes with a composite p≤0.01) by the Luminator gene expression analysis software package had a correlation of 0.847 (Spearman's Rho, p<0.0001, n=107, data not shown), whereas genes that were not called "signature" only exhibited a correlation of 0.435 (Spearman's Rho, p<0.0001, n=170, data not shown).
The readings from the quantitative scanning were analysed by the Affymetrix Gene Expression Analysis Software (Affymetrix).
Gene expression was evaluated by determining the relative quantity (ΔCT) of the mRNA using the gene expression analysis software provided with the iQ5 Cycler.
Pathway analysis to identify gene networks and biological processes affected by the gene expression changes was performed using Metacore software (Thomson Reuters).
The relative expression analysis and group-wise comparison of the target gene was performed by the Relative Expression Software Tool (REST, available at http://www.gene-quantification.com)[ 19].
In order to understand how PCGs and miRNAs expression patterns correlate with hematopoietic cell differentiation, both genome and miRNAs expression profiles were analyzed as global patterns by using the Gene Expression Dynamics Inspector (GEDI) software [ 24].
For the statistical analysis of relative gene expression the Relative Expression Software Tool was used.
By time-series gene expression measurements and our developed software BSIP and GeneNetwork, we reconstructed an apoptosis-related gene network.
Many diseases are characterized by altered gene expression.
To identify cytokines and transcription factors responsible for cardiomyogenic differentiation, 69 human cells were analyzed, depending on gene expression levels, by GeneSpringGX software, and clustered into 30 groups (Fig. 1A, Table 1).
