What Are Microarrays?DNA microarrays can be thought of as the massively parallel version of Northern blotting. While the Northern blotting technique is capable of analysing for each experiment the expression of one single gene in different conditions, microarrays allow the exploration of the expression levels of thousands of genes in several different conditions in one single run.
As Northern blotting and many other classic techniques widely used in molecular biology, the fundamental basis of DNA microarrays is the process of hybridization. Two strands of nucleic acid, DNA or RNA, hybridize if they are complementary to each other. This principle is exploited to measure the unknown quantity of one RNA or DNA molecule (target) on the basis of the amount of a complementary sequence (probe), that has hybridized to the target. The level of hybridization is usually quantified by measuring the level of a detectable chemical label, used to mark the target or the probe sequence in the experiment.
In the microarray technique, the probe sequences are immobilized on the surface, at a separation of a few micrometers so that is possible to place many different probes on a small single surface of one square centimeter. The sample is usually labeled with a fluorescent dye that can be detected by a light scanner that scans the surface of the chip.
Each probe sequence matches a particular messenger RNA present in the sample. The concentration of a specific RNA messenger is a result of expression of its corresponding gene. Observing all the microarray spots at the same time gives the expression profile of a sample, i.e. the complete picture of the expression of all the genes represented on the microarray.
Lots of useful information and links pertaining to microarrays
Stanford Microarray Database (SMD)
Stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.
SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches.
GeneCards integrates a subset of the information stored in major data sources dealing with human genes and their products (with a major focus on medical aspects). GeneCards allows the access to expression data extracted from ESTs libraries analysis
Gene Expression Omnibus
A public repository for a wide range of high-throughput experimental data. These data include single and dual channel microarray-based experiments measuring mRNA, genomic DNA and protein abundance, as well as non-array techniques such as serial analysis of gene expression (SAGE), and mass spectrometry proteomic data.
The Microarray Gene Expression Data (MGED) Society
An international organization of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments.
ArrayExpress is a public repository for microarray data. Besides the browsing and querying of the data it offers the possibility to export the data for further analysis with the EBI's free analysis software, Expression profiler
A set of tools for clustering, analysis and visualization of gene expression and other genomic data. Tools in the Expression Profiler allow to perform cluster analysis, pattern discovery, pattern visualization, study and search Gene Ontology categories, generate sequence logos, extract regulatory sequences, study protein interactions, as well as to link analysis results to external tools and databases.
An open source and open development software project for the analysis and comprehension of genomic data.
This is the public place for microarray protocol distribution.
Microbial Diagnostic Microarrays
A website on the application of microarrays for the detection, identification and community structure analysis of bacteria.
Canadian Microarray Resources
Where to find microarrays and fabrication labs in Canada
Resources for microarray analysis and gene expression profiling
- Epigenetics: Current Research and Emerging Trends
- Next-generation Sequencing: Current Technologies and Applications
- Genome Analysis: Current Procedures and Applications