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1646–1652 Nucleic Acids Research, 2006, Vol. 34, No. 5 doi:10.1093/nar/gkl068 Systematic identification of microRNA functions by combining target prediction and expression profiling Xiaowei Wang* and Xiaohui Wang Ambion, Inc., 2130 Woodward Street, Austin, TX 78744, USA Received February 7, 2006; Revised and Accepted March 1, 2006 ABSTRACT one of the most active research fields in biology. miRNAs function through suppressing the expression of their targeted Target predictions and validations are major obsta- genes. They are known to be involved in many diverse func- cles facing microRNA (miRNA) researchers. Animal tions such as regulation of cell proliferation, differentiation, miRNA target prediction is challenging because of apoptosis, carcinogenesis and viral infection (1–8). limited miRNA sequence complementarity to the Unfortunately most of the hundreds of newly identified targets. In addition, only a small number of predicted animal miRNAs have unknown functions (9). One major targets have been experimentally validated and the obstacle is to identify the targets regulated by miRNAs. Target miRNA mechanism is poorly understood. Here we prediction in plants is relatively straightforward because of present a novel algorithm for animal miRNA target the near-perfect alignment between a miRNA and its target prediction. The algorithm combines relevant para- sequence (10). In contrast, prediction of animal miRNA meters for miRNA target recognition and heuristic- targets is very challenging because there are onl