What algorithm is used for enrichment analysis?

All enrichment analysis in EcoToxXplorer is over-representation analysis (ORA), computed using hypergeometric tests. This test computes the probability that the list of differentially expressed genes contains more results from a particular gene set than would be expected if the list of DEGs were drawn randomly.

For gene set libraries, EcoToxXplorer supports gene set analysis of EcoToxModules and EcoToxProcesses. Other gene set libraries such as Gene Ontology do not contain enough representation from each pathway since the EcoToxChips have only 384 wells. Since the EcoToxModules and Processes are much larger, this is less of an issue.

Note, the conventional gene set enrichment analysis (GSEA) is not offered in EcoToxXplorer, as GSEA requires a complete ranked gene list, this is not the case here since the EcoToxChips have only 384 wells