GeneTerm Linker: Web based post enrichment association by non-redundant reciprocal linkage tool.
DAVID: Functional annotation, classification and Id conversion of gene expression data.
EASE: The stand-alone version of DAVID application for windows.
GSEA: Gene Set Enrichment Analysis. A tool with a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states.
HEFaLMP: a functional map of the human genome.
GOstat: Find statistically overrepresented GO terms within a group of genes.
ARACNE: Algorithm for the Reconstruction of Accurate Cellular Networks through the use of expresson profiles.
NetworKIN: NetworKIN is a method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins.
R / Bioconductor based packages: