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NanoMiner - integrative human transcriptomics data resource for nanoparticle research.

Lingjia Kong1, Soile Tuomela, Lauri Hahne

  • 1Department of Signal Processing, Tampere University of Technology, Tampere, Finland.

Plos One
|July 23, 2013
PubMed
Summary
This summary is machine-generated.

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NanoMiner is a new web resource for analyzing nanoparticle exposure transcriptomics data. It provides a standardized database of 404 human samples, enabling researchers to explore gene expression and identify nanoparticle impacts.

Area of Science:

  • Environmental toxicology
  • Genomics
  • Bioinformatics

Background:

  • Nanoparticle research generates vast amounts of transcriptomics data.
  • Integrating this data is crucial for understanding nanoparticle impacts on human health and the environment.
  • Existing data is often fragmented and difficult to analyze collectively.

Purpose of the Study:

  • To develop a centralized, user-friendly web resource for nanoparticle transcriptomics data.
  • To facilitate systematic analysis and data mining of existing microarray datasets.
  • To enable researchers to investigate gene expression changes induced by various nanoparticles.

Main Methods:

  • Collected and curated 404 human transcriptome samples exposed to nanoparticles.
  • Standardized data annotation, preprocessing, and normalization.

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  • Developed a web interface (NanoMiner) for data exploration and analysis.

    • Main Results:

    • NanoMiner offers tools to search and plot gene expression profiles.
    • Users can cluster samples, identify differentially expressed genes, and detect causative nanoparticles.
    • The resource allows analysis of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) terms.

    Conclusions:

    • NanoMiner provides a valuable, standardized repository for nanoparticle-related transcriptomics data.
    • The resource enhances the utility of existing data for broader research contexts.
    • It supports systematic analysis of gene expression and biological pathways affected by nanoparticles.