Methods im Molecular Biology miRNA expression landscapes in stem cells, tissues and cancer

miRNAs play critical roles in the regulation of gene expression with two major functions: degrading mRNA in a sequence specific manner or repressing its translation. Publicly available data sets on miRNA and mRNA expression in embryonal and induced stem cells, human tissues and solid tumors are analyzed in this case study using self organizing maps (SOM) to characterize miRNA expression landscapes in the context of cell fate commitment, tissue specific differentiation and its dysfunction in cancer. The SOM portraits of the individual samples clearly reveal groups of miRNA specifically overexpressed without the need of additional pairwise comparisons between the different systems. Sets of miRNA differentially over and underexpressed in different systems are provided. The individual portraying of the expression landscapes enables a very intuitive, image-based perception which clearly promotes the discovery of qualitative relationships between the systems studied. We see perspectives for broad applications of this method in standard analysis to many kinds of high throughput data of single miRNA and especially combined miRNA/mRNA data sets.