For example, GRNs could be drawn from microarray data consisting of 62 primary tumors and 41 normal prostate tissues to explore the significant GRNs correlated with disease, severity and stage in the prostate cancer [23].
The preprocessing procedure for the raw microarray data consists of background correction, normalization, and summarization.
The preprocessing procedure for the raw microarray data consists of back-ground correction, normalization, and summarization.
Microarray data, consisting of 52 antigens for melanoma (CD45−) samples and 78 antigens for leukocytes (CD45+), were median normalized separately.
For prostate cancer, the cDNA microarray data consist of 62 tumors and 41 normal prostate samples (Lapointe et al., 2004), while the oligo microarray (Affymetrix U95Av2) data contain 52 tumor and 50 non-tumor samples (Singh et al., 2002).
Here, we employed this module-based approach for the estimation of temporal transcription regulation structure of A. fumigatus in heat shock with microarray data consisting of very short length of time point, i.e., 6.
For lung cancer, the cDNA microarray data consist of 13 squamous cell lung cancer and five normal lung specimens (Garber et al., 2001), while the data by Affymetrix human U95A oligonucleotide arrays consist of 21 squamous cell lung carcinomas and 17 normal lung specimens (Bhattacharjee et al., 2001).
Arabidopsis thaliana (Arabidopsis) microarray expression data consisting of 22,810 probe sets (genes) and 216 samples under five conditions (control, cold, drought, heat, and salt) were analyzed.
Since every slide was printed with two full replicates of the microarray, each microarray data set consisted of four dye-balanced hybridizations for each type of xylem in duplicate.
The microarray data analysis consisted of the following steps: 1. quantile method normalization, 2. global clustering and PCA-analysis, 3. fitting the data to a linear model, 4. detection of differential gene expression and 5. over-representation analysis of differentially expressed genes.
