Faculty Collaboration Database

miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy. PLoS One 2015;10(11):e0143066

Date

11/17/2015

Pubmed ID

26571139

Pubmed Central ID

PMC4646525

DOI

10.1371/journal.pone.0143066

Scopus ID

2-s2.0-84957110827 (requires institutional sign-in at Scopus site)   68 Citations

Abstract

Small RNA RNA-seq for microRNAs (miRNAs) is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries. miRNAs are summarized at the level of raw reads in addition to reads per million (RPM). Reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA) are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. miRge was designed to optimally identify miRNA isomiRs and employs an entropy based statistical measurement to identify differential production of isomiRs. This allowed us to identify decreasing entropy in isomiRs as stem cells mature into retinal pigment epithelial cells. Conversely, we show that pancreatic tumor miRNAs have similar entropy to matched normal pancreatic tissues. In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench), miRge was faster (4 to 32-fold) and was among the top-two methods in maximally aligning miRNAs reads per sample. Moreover, miRge has no inherent limits to its multiplexing. miRge was capable of simultaneously analyzing 100 small RNA-Seq samples in 52 minutes, providing an integrated analysis of miRNA expression across all samples. As miRge was designed for analysis of single as well as multiple samples, miRge is an ideal tool for high and low-throughput users. miRge is freely available at http://atlas.pathology.jhu.edu/baras/miRge.html.

Author List

Baras AS, Mitchell CJ, Myers JR, Gupta S, Weng LC, Ashton JM, Cornish TC, Pandey A, Halushka MK

Author

Toby Charles Cornish MD, PhD Professor in the Pathology department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Animals
Base Sequence
Cell Differentiation
Cells, Cultured
Computational Biology
Embryonic Stem Cells
Entropy
Humans
Mice
MicroRNAs
Retinal Pigment Epithelium
Sequence Analysis, RNA
Software