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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

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Profiling of Estrogen-regulated MicroRNAs in Breast Cancer Cells
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Published on: February 21, 2014

miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.

Wei-Chi Wang1, Feng-Mao Lin, Wen-Chi Chang

  • 1Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China. canser.bi95g@nctu.edu.tw

BMC Bioinformatics
|October 14, 2009
PubMed
Summary
This summary is machine-generated.

We developed miRExpress, a novel software tool for analyzing microRNA (miRNA) expression profiles from high-throughput sequencing data. This efficient method aids in discovering new miRNAs and understanding gene regulation in various species.

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Published on: August 3, 2011

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) are key regulators of gene expression in animals and plants.
  • Oligonucleotide microarrays detect known miRNA expression but cannot discover novel miRNAs.
  • Second-generation sequencing offers a sensitive, high-throughput method for small RNA analysis and novel miRNA discovery.

Purpose of the Study:

  • To develop a systematic approach for extracting miRNA expression profiles from second-generation sequencing data.
  • To create a user-friendly software package for miRNA expression analysis without requiring sequenced genomes.
  • To establish an efficient and flexible tool for investigating miRNA regulation and discovering novel miRNAs.

Main Methods:

  • Implementation of miRExpress, a stand-alone software package for miRNA expression profiling.
  • Utilizing high-throughput sequencing reads as input for the miRExpress software.
  • Demonstrating the software's utility with two Illumina sequencing datasets from human and plant species.

Main Results:

  • miRExpress successfully extracts miRNA expression profiles from sequencing reads.
  • The software operates efficiently and flexibly, supporting database integration.
  • The approach is effective for both known and novel miRNA identification across different species.

Conclusions:

  • miRExpress is a robust, database-supported tool for miRNA expression profiling.
  • The software facilitates the discovery of novel miRNAs and enhances the understanding of miRNA regulation.
  • The effectiveness of miRExpress is validated through human and plant expression data analysis.