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Reporter Genes02:11

Reporter Genes

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Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
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Phantasus, a web application for visual and interactive gene expression analysis.

Maksim Kleverov1,2, Daria Zenkova1, Vladislav Kamenev1

  • 1ITMO University, Computer Technologies Laboratory, Saint Petersburg, Russian Federation.

Elife
|May 14, 2024
PubMed
Summary

Phantasus is a user-friendly web application simplifying gene expression analysis. It provides access to over 96,000 public datasets and supports user-uploaded data for comprehensive analysis.

Keywords:
computational biologygene expressioninteractive analysisnonepublic datareanalysissystems biologyvisualization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Transcriptomic profiling generates vast gene expression datasets.
  • Analyzing these datasets requires significant technical expertise.
  • Publicly available gene expression data offers valuable research opportunities.

Purpose of the Study:

  • To present Phantasus, a web application for interactive gene expression analysis.
  • To provide streamlined access to over 96,000 public gene expression datasets.
  • To enable analysis of both public and user-uploaded gene expression data.

Main Methods:

  • Development of a user-friendly web application (Phantasus).
  • Integration of an interactive JavaScript-based heatmap interface.
  • Incorporation of R-based analysis methods for sophisticated computations.
  • Support for data loading, normalization, filtering, differential gene expression, and downstream analysis.

Main Results:

  • Phantasus offers interactive visualization of gene expression data.
  • The application allows seamless integration of public and private datasets.
  • Users can perform complex analyses from data preprocessing to downstream interpretation.

Conclusions:

  • Phantasus democratizes gene expression data analysis.
  • The tool enhances the accessibility and utility of large-scale transcriptomic datasets.
  • Phantasus facilitates efficient exploration of cell states and biological insights.