Identification of RNAa characteristics using gene expression ominibus

Abstract

RNA activation (RNAa) is a biological process characterized by miRNAs (microRNAs) binding to gene promoters and resulting in up regulation. RNAa is a key to cure virus infection and metabolic diseases such as HIV and cancer. However, the role of RNAa remains largely unknown. Very few cases have been reported in the past decade. In contrast to wet-lab approach which is costly and time consuming, we have performed a computer-based analysis to identify miRNAs that may activate transcription through Argonaute2 (Ago2). All microarray data are collected from Gene Expression Omnibus (GEO). We aim to find the genes that are commonly 1) up-regulated in a miRNA transfection experiment and 2) down-regulated in an Ago2 knockdown experiment. Finally we have performed local sequence alignment between the transfected miRNA and the gene promoters. Smith-Waterman (SW) algorithm is employed to find the best alignment score. Our findings show at least 6 miRNAs that could bind on promoters and may activate transcription.