PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes).

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.

OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.

MAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.

ISACGH (In Silico Array CGH) is a tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included in the GEPAS package.

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.

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles.

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally.