Bioinformatics Links Directory : Microarrays

This section contains links to microarray methods, standards for microarray data, and analysis tools for expression data.

BiologicalNetworks - (Found July 2, 2008 )

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.
http://brak.sdsc.edu/pub/BiologicalNetworks/

Asterias - (Found July 2, 2008 )

Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.
http://asterias.bioinfo.cnio.es/

ASIAN - (Found July 2, 2008 )

ASIAN (Automatic System for Inferring a Network) is a server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling.
http://eureka.ims.u-tokyo.ac.jp/asian/

ArrayXPath - (Found July 2, 2008 )

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.
http://www.snubi.org/software/ArrayXPath/

ArrayProspector - (Found July 2, 2008 )

ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.
http://string.embl-heidelberg.de:8080/prophecies_html/prophecies.html

ArrayPipe - (Found July 2, 2008 )

ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.
http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl

ArrayExpress - (Found July 2, 2008 )

Public repository for microarray based gene expression data; contains several curated gene expression datasets.
http://www.ebi.ac.uk/arrayexpress/

Build your own arrayer - (Found July 2, 2008 )

The MGuide (version 2.0). The Brown Labs complete guide to microarraying for the molecular biologist.
http://cmgm.stanford.edu/pbrown/mguide/index.html

Canadian Microarray Resources - (Found July 2, 2008 )

Contact information, availabilities and expertise of Canadian microarray centres; includes labs that supply cDNA or oligonucleotide spotted arrays and other services, and labs that can analyse RNA with Affymetrix chips.
http://kinase.uhnres.utoronto.ca/CanArrays.html

CAPweb - (Found July 2, 2008 )

CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.
http://bioinfo.curie.fr/CAPweb/