Integrating microarray data and gene regulatory networks: Survey and critical considerations

Microarray gene expression and gene regulatory interactions are two of the most significant data sources in the areas of molecular biology and biotechnology. In this article we survey existing methods and tools supporting the integration of these two data sources. We start with gene regulatory network reconstruction methods focusing on the reconstruction using microarray experiments. Then we discuss methods and tools for gene expression data analysis based on gene regulatory network knowledge and we review algorithms and tools for gene regulatory networks selection using microarray data. Finally we introduce a new methodology for the identification of differentially expressed functional paths or sub-paths within a gene regulatory network using microarray data analysis.