GO-Elite is designed to identify a minimal non-redundant set of biological Ontology terms or pathways to describe a particular set of genes or metabolites.
Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of “seq2gene” and “gene2path” components.
::DEVELOPER
Xinan Yang <xyang2 at uchicago.edu>; Bin Wang <binw at uchicago.edu>
PathVisioRPC is an XML-RPC interface for the pathway analysis tool PathVisio. It allows you to use PathVisio functions to create pathways and visualise and analyse data on pathways in your familiar analytical environment (R, Python, Perl, C++, so on …)
LRpath performs gene set enrichment testing using logistic regression, and allows the data to remain on a continuous scale. This web-based tool tests against several annotation databases, including Gene Ontology, multiple pathway databases, metabolite, transcription factor and microRNA target sets, and literature-derived annotations. LRpath also includes clustering analysis functionality, allowing you to identify and compare biological concept signatures across multiple studies. LRpath performs well with both small and large sample sizes. Additional benefits of using the LRpath program include (1) the ability to perform both “directional” and “non-directional” enrichment tests that allow for two different perspectives and (2) the ability to easily compare and visualize results across multiple studies using LRpath clustering.
RNA-Enrich is faster than LRpath and best for RNA-seq data that exhibit a relationship between gene read counts and significance of differential gene expression (e.g. genes with higher read counts may have more significant p-values, and vice versa).
MetPA (Metabolomics Pathway Analysis) is a free and easy-to-use web application designed to perform pathway analysis and visualization of quantitative metabolomic data
GEPAT (Genome Expression Pathway Analysis Tool) is a modular, scalable and professional-grade software integrating analysis and interpretation of microarray gene expression data.