LRpath / RNA-Enrich
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).
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RNA-Enrich: A cut-off free functional enrichment testing method for RNA-seq with improved detection power.
Lee C, Patil S, Sartor MA.
Bioinformatics. 2015 Nov 25. pii: btv694.
BMC Genomics. 2012 Oct 4;13:526. doi: 10.1186/1471-2164-13-526.
LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types.
Kim JH1, Karnovsky A, Mahavisno V, Weymouth T, Pande M, Dolinoy DC, Rozek LS, Sartor MA.