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DNA Microarrays

DNA Microarrays

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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Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

What is Gene Expression?

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...

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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 microarray-based...

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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics

Misha Kapushesky¹, Tomasz Adamusiak, Tony Burdett

¹European Bioinformatics Institute, EMBL, Hinxton, UK and Dana-Farber Cancer Institute, Boston, MA, USA.

Nucleic Acids Research

|November 9, 2011

Summary

This summary is machine-generated.

The Gene Expression Atlas is a database that provides gene expression data across various conditions and species. It is regularly updated with new data, offering insights into differential gene expression.

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Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

The Gene Expression Atlas (GEA) is a valuable resource for accessing gene expression data.
It integrates data from ArrayExpress and the European Nucleotide Archive.
The database covers diverse biological and experimental conditions.

Purpose of the Study:

To provide an updated overview of the Gene Expression Atlas database.
To highlight its features for querying differential gene expression.
To showcase the database's growth in terms of species, conditions, and studies.

Main Methods:

Data curation and re-annotation from public archives.
Statistical analysis of gene expression data.
Development of a user-friendly interface for data retrieval.

Main Results:

As of August 2011 (Release 11.08), the database supports 19 species.
Contains expression data for 19,014 biological conditions across 136,551 assays from 5,598 studies.
20 monthly releases have been implemented since the previous report.

Conclusions:

The Gene Expression Atlas is a comprehensive and expanding resource for gene expression analysis.
Its updated content and improved interface facilitate biological research.
The database supports a wide range of queries related to gene expression patterns.