Methods and software Pathway analysis

1 methods , software

1.1 over-representation analysis or enrichment analysis (ora)
1.2 functional class scoring (fcs)
1.3 pathway topology (pt)

methods , software

pathway analysis software can divided web-based applications, desktop programs , programming packages. programming packages coded in r , python languages, , shared openly through bioconductor , github projects. different methods of pathway analysis evolve fast, classification of these methods still discussable. there 3 main groups of methods in pathway analysis according to: ora, fsc , pt.

over-representation analysis or enrichment analysis (ora)

this method measures percentage of genes in pathway or gene group (gene ontology (go) groups, protein families, pathways) have differential expression. aim of ora list of relevant pathways, ordered in accordance p-value. basic hypothesis in ora relevant pathways can identified number of genes differently expressed in experiment pathways contain. statistical significance of overlap between genes pathway , list of differently expressed genes determined such statistical tests fisher s exact test, hypergeometric distribution test or jaccard index.

functional class scoring (fcs)

this method analyzes expression change of overall genes in list (not ranking statistical significance or else) of differently expressed in experiment genes. fcs discards ora cut-off threshold limitation. aim of fcs evaluate differently expressed genes enrichment scores (see gene set enrichment) using pathways gene sets perform computations. 1 of first , popular methods deploying fcs approach gene set enrichment analysis (gsea).

pathway topology (pt)

pathway topology same fcs, except pt uses gene-level statistics through different databases integration. critical difference leveraging information role, position, , direction of interaction pathway database, pt able re-score significance of pathway linkages change, whereas fcs provide same score. examples pt approaches include signaling pathway impact analysis (spia), enrichnet, ggea, , topogsa.