Bioinformatics Links Directory : Microarrays

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

GeneTrail - (Found July 2, 2008 )

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.
http://genetrail.bioinf.uni-sb.de/index.php

GenePublisher - (Found July 2, 2008 )

GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.
http://www.cbs.dtu.dk/services/GenePublisher

Gene Expression Data Analyzer - (Found July 2, 2008 )

The Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization.
http://bioinformatics.upmc.edu/GE2/GEDA.html

GEMS - (Found July 2, 2008 )

GEMS (Gene Expression Mining Server) is a tool for biclustering microarray data. It is available as a web tool and as a standalone command-line program.
http://genomics10.bu.edu/terrence/gems/

ExpressYourself - (Found July 2, 2008 )

ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.
http://array.mbb.yale.edu/analysis/

Expression Profiler - (Found July 2, 2008 )

Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.
http://www.ebi.ac.uk/expressionprofiler/

Doelan - (Found July 2, 2008 )

Doelan is an tool designed to monitor the quality of DNA microarray production.
http://www.transcriptome.ens.fr/doelan/

CIBEX - (Found July 2, 2008 )

The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard.
http://cibex.nig.ac.jp/

ChipInfo - (Found July 2, 2008 )

ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.
http://biosun1.harvard.edu/complab/chipinfo/

CARMAweb - (Found July 2, 2008 )

Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.
https://carmaweb.genome.tugraz.at/carma/