Analysis pipeline. By comparing the microarray profiles of miRNA-expressing cells and mock transduced cells, genes with significant changes were identified. The down-regulated genes with predicted miRNA binding sites were categorized as putative direct targets of miR-K12-11/miR-155. For direct targets that are known transcription factors, transcription factor binding sites (TFBS) were searched in the promoter regions of other affected genes. For those indirect targets, motif analysis within their sequences identified potential regulators. In addition, Gene Ontology and known protein-protein interactions help to build the gene regulatory networks (GRNs).