Analysis of targets and functions coregulated by microRNAs

Shu-Jen Chen, Hua-Chien Chen
Methods in Molecular Biology 2011, 676: 225-41
MicroRNAs (miRNAs) are small, nonprotein-coding RNAs that negatively regulate their mRNA target genes in a sequence-specific manner. While their specific impact on biological processes and cellular functions remain largely unknown, dysregulated miRNAs have been implicated in numerous diseases, including cancers. Several large-scale profiling studies using tissue samples have revealed a consistent yet complex pattern of miRNA dysregulation in human cancer. In particular, global alteration of multiple miRNAs is common in human tumorigenesis. Systemic analysis of pathways and functions coregulated by these dysregulated miRNAs is a crucial step to understand the role of miRNAs in tumorigenesis. This chapter provides an integrated pipeline to identify cellular pathways and functions specifically regulated by multiple dysregulated miRNAs. Protocols described in this chapter include (1) miRNA target prediction using TargetScan algorithm, (2) data compilation to identify target genes coregulated by multiple miRNAs, and (3) pathway enrichment analysis of coregulated targets using MetaCore pathway and network database.

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