BioDiscovery this week released Nexus Expression, a software tool for gene expression analysis. The product supports all array platforms including Affymetrix, Agilent, Illumina, Roche NimbleGen, and custom arrays.
According to BioDiscovery, Nexus Expression enables users to cluster genes and samples to discover expression patterns, compare expression profiles of multiple comparisons alongside gene annotations, display significant genes in affected biological processes, and perform enrichment analysis to identify genes that are significantly overrepresented in a population.
Developers at Memorial Sloan-Kettering Cancer Center and the University of Toronto have released a new Cytoscape plug-in called ExpressionCorrelation, which creates a network from gene expression data.
It computes a similarity network from either the genes or conditions in a gene expression matrix. The nodes in the similarity network represent genes or conditions and the edges represent the similarity between vectors of the expression levels of genes across all given conditions, in the case of a gene correlation network, or the similarity between vectors of the expression levels of all genes in a single condition, in the case of a condition correlation network.
The plug-in allows users to select an expression matrix of microarray data directly from Cytoscape, computes the similarity matrix using the Pearson correlation coefficient, and converts it to an interaction network in Cytoscape.