GenePattern is a software package for the analysis of molecular profiles, e.g., genome-wide microarray expression signatures. It includes a collection of analytic and visualization tools, interfaces for the easy construction of analytic pipelines and integration of new modules without additional programming. Gene Pattern is available for MacOS, Windows, and Linux platforms.
Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA is available for any operating system (Windows, Mac, Linux) in a variety of implementations, including a Java desktop application, a jar file, an R package, or a GenePattern module.
GeneCruiser provides integrated access to the gene and microarray feature information freely available from public databases. It allows users to retrieve annotations from various databases (LocusLink, RefSeq, SwissProt) using Affymetrix probe identifiers, or convert genes from accession numbers or keywords into matching probe IDs on one or more microarray chips. GeneCruiser is a web service accessible through a web interface, and is also available as a GenePattern module.
The Connectivity Map (also known as cmap) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of decisive functional connections between drugs, genes and diseases through the transitory feature of common gene expression changes. It is deployed through a web interface designed to allow biologists, pharmacologists, chemists and clinical scientists the opportunity to use cmap without the need for any specialist ability in the analysis of gene expression data.