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The Eukaryotic Promoter Region

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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

The Eukaryotic Promoter Region

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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: Feb 19, 2026

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

Bringing numerous methods for expression and promoter analysis to a public cloud computing service.

Krzysztof Polanski¹, Bo Gao¹, Sam A Mason²

¹Department of Statistics.

Bioinformatics (Oxford, England)

|November 11, 2017

Summary

Researchers have containerized 14 popular bioinformatics algorithms using Docker, making them accessible via the CyVerse Discovery Environment. This improves the usability and reproducibility of computational methods for expression and promoter analysis.

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Microarray Analysis for Saccharomyces cerevisiae

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Microarray Analysis for Saccharomyces cerevisiae

Microarray Analysis for Saccharomyces cerevisiae

Published on: April 7, 2011

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Novel algorithms are frequently introduced but face challenges in cross-institutional use due to implementation and dependency issues.
Public cloud platforms offer a solution by hosting reproducible computational tools in self-contained environments.

Purpose of the Study:

To enhance the accessibility and usability of popular bioinformatics algorithms.
To address challenges in implementing and sharing computational methods across research groups.

Main Methods:

14 widely-used bioinformatics algorithms, primarily for expression and promoter analysis, were selected.
These algorithms were implemented to a high standard and packaged into isolated Docker containers.
The containerized tools were integrated into the CyVerse Discovery Environment.

Main Results:

A collection of 14 well-implemented bioinformatics tools is now available.
These tools are accessible through the CyVerse Discovery Environment, facilitating wider use.
The project successfully leveraged Docker and cloud computing for method dissemination.

Conclusions:

Containerization and cloud integration significantly improve the accessibility and reproducibility of bioinformatics tools.
The CyVerse UK project provides a scalable model for sharing computational methods in biological research.