SiGPAT is a useful tool based on gene set analysis for microarray data. It can find significant expression patterns of gene sets by pri-defined biological knowledge. To be unique to other tools, SiGPAT assignes two statistics for each gene sets and classifies expression patterns of gene sets form two dimension distribution of set-level statistics. The tool was evaluated with better performance than current tools such as GSEA and SAM-GS
Moksiskaan is a generic database that can be used to integrate information about the connections between genes, proteins, pathways, drugs, and other biological entities. Moksiskaan provides various pathway components for Anduril and may be used to extends its capabilities.
MEGA-V is an open-source R application with a Shiny web interface. It identifies gene sets with a significantly higher number of variants in a cohort of interest (cohort A) as compared to (1) a control cohort (cohort B) or (2) a random distribution generated using Monte Carlo.
Broad-Enrich tests sets of broad genomic regions (e.g., from ChIP-seq data for histone modifications or copy number variations) for enriched biological pathways, Gene Ontology terms, or other gene sets.
TopoGSA (Topology-based Gene Set Analysis) computes and visualise the topological properties of a set of genes/proteins mapped onto a molecular interaction network. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, are computed and compared against those of known cellular pathways and processes (KEGG, BioCarta, GO, etc.).