Urgent need for consistent standards in functional enrichment analysis.

ABSTRACT: Gene set enrichment tests (a.k.a. functional enrichment analysis) are among the most frequently used methods in computational biology. Despite this popularity, there are concerns that these methods are being applied incorrectly and the results of some peer-reviewed publications are unreliable. These problems include the use of inappropriate background gene lists, lack of false discovery rate correction and lack of methodological detail. To ascertain the frequency of these issues in the literature, we performed a screen of 186 open-access research articles describing functional enrichment results. We find that 95% of analyses using over-representation tests did not implement an appropriate background gene list or did not describe this in the methods. Failure to perform p-value correction fo

SUBMITTER: Wijesooriya K 

PROVIDER: S-EPMC8936487 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature