Molecular Networks in Microarray Analysis

Microarray-based characterization of tissues, cellular and disease states, and environmental condition and treatment responses provides genome-wide snapshots containing large amounts of invaluable information. However, the lack of inherent structure within the data and strong noise make extracting and interpreting this information and formulating and prioritizing domain relevant hypotheses difficult tasks. Integration with different types of biological data is required to place the expression measurements into a biologically meaningful context. A few approaches in microarray data interpretation are discussed with the emphasis on the use of molecular network information. Statistical procedures are demonstrated that superimpose expression data onto the transcription regulation network mined from scientific literature and aim at selecting transcription regulators with significant patterns of expression changes downstream. Tests are suggested that take into account network topology and signs of transcription regulation effects. The approaches are illustrated using two different expression datasets, the performance is compared, and biological relevance of the predictions is discussed.