Dec

23

MicroRNA Discovery & Analysis by High-Throughput Sequencing

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For profiling microRNA expression, microarrays have been the standard technology. However, the recent introduction of deep sequencing technology, enabling the simultaneous sequencing of up to millions of DNA or RNA molecules, has provided another option for profiling microRNAs. Deep sequencing utilizes massively parallel sequencing, generating millions of small RNA sequence reads from a given sample. Profiling of microRNAs by deep sequencing measures absolute abundance and allows for the discovery of novel microRNAs that have eluded previous cloning and standard sequencing efforts.[1]

There are many web-based tools available for handling microRNA deep sequencing data:

mirTools – a web server for microRNA profiling and discovery based on high-throughput sequencing data.

miRDeep – Discovering known and novel miRNAs from deep sequencing data

deepBase – a database for deeply annotating and mining deep sequencing data

miRExpress – Analyzing high-throughput sequencing data for profiling microRNA expression

miRanalyzer – A microRNA detection and analysis tool for next-generation sequencing experiments

CID-miRNA – Computational Identification of microRNA

miRCat – miRNA Categorizer

  1. Creighton CJ, Reid JG, Gunaratne PH. (2009) Expression profiling of microRNAs by deep sequencing. Brief Bioinform 10(5), 490-97. [abstract]

Oct

14

Integrating microRNA and mRNA expression profiles for identification of regulatory networks

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The discovery of microRNA as an additional regulatory mechanism has been a revolution to the field of Developmental Biology. While early research has focused on the identification of miRNAs using a combination of experimental and computational techniques, subsequent studies have focused on identification of miRNA-target mRNA pairs as a means of identifying regulatory networks. It has been shown that the relationship between messenger RNA and microRNA (often an inverse relationship) plays a large role in cell functionality, especially in the early stages of cell development.  Read more