MicroRNA Expression Landscapes in Stem Cells, Tissues, and Cancer

MicroRNAs play critical roles in the regulation of gene expression with two major functions: marking mRNA for degradation in a sequence-specific manner or repressing 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 (SOMs) 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 have been detected in this study. The individual portraits of the expression landscapes enable 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.