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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: Sep 10, 2025

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

Gene-set enrichment analysis and visualization on the web using EnrichmentMap:RNASeq.

Max Franz¹, Christian T Lopes¹, Mike Kucera¹

¹The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.

Bioinformatics Advances

|August 27, 2025

Summary

EnrichmentMap: RNASeq offers a user-friendly, web-based gene-set enrichment analysis for RNA sequencing experiments. This tool simplifies complex analysis for biologists, requiring no software installation.

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Last Updated: Sep 10, 2025

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

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Published on: December 2, 2009

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research

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Published on: August 16, 2017

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Gene-set enrichment analysis (GSEA) is crucial for interpreting RNA sequencing (RNA-Seq) data.
Existing GSEA tools can be computationally intensive and require software installation, posing a barrier for biologists.
There is a need for accessible and efficient GSEA tools tailored for specific experimental designs like two-case RNA-Seq.

Purpose of the Study:

To introduce EnrichmentMap: RNASeq, a novel web-based application for gene-set enrichment analysis.
To provide a simplified and faster alternative to desktop software for RNA-Seq data analysis.
To enhance the accessibility of GSEA for biologists with limited computational expertise.

Main Methods:

Development of a web-based application, EnrichmentMap: RNASeq.
Implementation of a simplified user interface for intuitive operation.
Integration with Cytoscape as a web app for interoperability.

Main Results:

EnrichmentMap: RNASeq provides an intuitive platform for gene-set enrichment analysis and visualization.
The application offers faster processing times compared to traditional desktop workflows.
It eliminates the need for software installation, making it readily accessible.

Conclusions:

EnrichmentMap: RNASeq effectively supports two-case RNA-Seq experiments for Homo sapiens.
The tool democratizes GSEA by catering to biologists with minimal computational background.
It represents a significant advancement in web-based bioinformatics tools for genomic data analysis.