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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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Gene Set Knowledge Discovery with Enrichr.

Zhuorui Xie1, Allison Bailey1, Maxim V Kuleshov1

  • 1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York.

Current Protocols
|March 29, 2021
PubMed
Summary
This summary is machine-generated.

Enrichr is a gene set enrichment analysis tool that helps researchers interpret large gene lists from various biological studies. It integrates numerous gene sets for comprehensive analysis and offers programmatic access and website integration.

Keywords:
bioinformaticsdiseasedrug discoveryenrichment analysisgene setsvisualizationweb application

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput biological studies generate vast lists of genes and proteins requiring interpretation.
  • Integrating omics data (genomics, transcriptomics, proteomics, etc.) with existing biological knowledge is crucial.
  • Enrichr serves as a gene set search engine to facilitate this interpretation.

Purpose of the Study:

  • To provide a comprehensive overview of the Enrichr platform's capabilities.
  • To detail protocols for utilizing Enrichr in various biological data analysis scenarios.
  • To highlight Enrichr's features for programmatic use and web integration.

Main Methods:

  • Utilizing Enrichr for analyzing gene lists from transcriptomics, proteomics, and GWAS studies.
  • Searching Enrichr using single genes or keywords.
  • Preparing RNA-seq data via BioJupies for Enrichr analysis.
  • Employing modEnrichr for model organism gene set analysis.
  • Integrating Enrichr with other tools like Geneshot and ARCHS4.
  • Visualizing enrichment results using Appyter.
  • Leveraging the Enrichr API for programmatic access.
  • Embedding an Enrichr button on websites.

Main Results:

  • Enrichr provides access to hundreds of thousands of annotated gene sets.
  • The platform synthesizes information from multiple high-profile projects.
  • Enrichr offers diverse methods for gene set enrichment computation and interactive visualization.
  • Protocols cover analysis of various data types and integration with other bioinformatics tools.

Conclusions:

  • Enrichr is a versatile tool for gene set enrichment analysis, supporting diverse research needs.
  • Its extensive gene set library and integration capabilities aid in understanding complex biological data.
  • Enrichr facilitates both direct analysis and programmatic integration into other platforms and websites.