For this, we first identified the probesets present on the Affymetrix microarray chip corresponding to each TF encoding gene loci.
If one gene probe on the microarray chip corresponded to more than one gene (e.g. multiple isoforms of a gene), all the corresponding genes were considered for functional analysis.
Both datasets included only ER IHC information, so the other four IHC results (PR, HER2, CK5/6 and EGFR) were dichotomized into 'positive ' and 'negative ' by the mRNA expression levels of the corresponding genes on the microarray chips.
In addition, the EST sequences and the corresponding clones have been used to develop various microarray chips based on spotted cDNA clones [ 9].
Microarray chips were scanned using a DNA Microarray Scanner (Agilent Technologies).
Microarray chips and reagents used in the experiment of a given colony were from the same Affymetrix batch.
Genome-wide studies using microarray chips to identify copy number changes in human cancer are becoming more common.
The microarray chips were scanned with GeneChip® scanner (Affymetrix).
Commercially available microarray chips for mouse genes (Agilent MouseGE 4 × 44 K, Agilent Technologies) were used.
In biology, high throughput gene expression data obtained from microarray chips forms a matrix [13].
