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We also obtained RNA-seq based gene expression data (RPKM) from64 and17 for mESC and pro-B cells, respectively.

The quality of DNA microarray based gene expression data relies on the reproducibility of several steps in a microarray experiment.

For that purpose tissue samples from 21 patients with resectable adenocarcinomas were collected for use in whole genome-microarray based gene expression analysis.

Subsequent differentiation of these mixed cultures would fail to generate single pure lineages needed for transplantation, modeling or population based gene expression studies (e.g. RNA-seq).

Genes with significant D (tissue) effect are said to show significant tissue based gene expression difference.

This utilises both predicted transcription factor binding sites (TFBS), transcription factor abundance, and our microarray based gene expression data.

The 'One-Color Microarray-Based Gene Expression Analysis' protocol Version 5.7 (Agilent Technologies, CA, USA) was followed.

RNA was isolated two days post-transfection, and microarray based gene expression analysis carried out (Fig. 9B).

Hybridization was carried out following the 'One-Color Microarray-Based Gene Expression Analysis' protocol Version 5.7 (Agilent Technologies, CA, USA).

RNAseq based gene expression data is the data platform of choice for a GRN inference.

To evaluate pathway based gene expression similarity measuring method, we conducted cell type classification test.