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RNASeqExpressionBrowser--a web interface to browse and visualize high-throughput expression data.

Thomas Nussbaumer1, Karl G Kugler1, Kai C Bader1

  • 1Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Center Munich, National Research Center for Environment and Health, 85764 Neuherberg, Germany.

Bioinformatics (Oxford, England)
|May 17, 2014
PubMed
Summary
This summary is machine-generated.

RNA sequencing (RNA-seq) analysis generates large datasets. The RNASeqExpressionBrowser is a new web tool simplifying access to RNA-seq expression data for non-experts, enabling easier gene exploration.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • RNA sequencing (RNA-seq) generates vast amounts of gene expression data.
  • Existing analysis pipelines like Tophat and Cufflinks produce complex outputs.
  • Accessing and interpreting RNA-seq data can be difficult for researchers without specialized bioinformatics expertise.

Purpose of the Study:

  • To develop an accessible, open-source web interface for exploring RNA-seq expression data.
  • To simplify the handling and visualization of analytical outputs from RNA-seq pipelines.
  • To provide a user-friendly platform for researchers to access and analyze gene expression patterns.

Main Methods:

  • Developed the RNASeqExpressionBrowser, a web-based interface.
  • The tool accepts gene expression data in a matrix-like format.
  • Implemented functionalities for browsing genes by identifiers, annotations, and sequence similarity.

Main Results:

  • The RNASeqExpressionBrowser allows flexible access to RNA-seq expression analysis outputs.
  • Users can easily search and view gene expression information.
  • A demonstration version is available, showcasing barley genome expression data.

Conclusions:

  • The RNASeqExpressionBrowser enhances the accessibility of RNA-seq data analysis.
  • This tool empowers non-experts to explore complex gene expression datasets.
  • The open-source nature facilitates wider adoption and application in biological research.