MOTIVATION: Microarray data analysis has expanded from testing individual genes for differential expression to testing gene sets for differential expression. The tests at the gene set level may focus on multivariate expression changes or on the differential expression of at least one gene in the gene set. These tests may be powerful at detecting subtle changes in expression, but findings at the gene set level need to be examined further to understand whether they are informative and if so how. RESULTS: We propose to first test for differential expression at the gene set level but then proceed to test for differential expression of individual genes within discovered gene sets. We introduce the overall false discovery rate (OFDR) as an appropriate error rate to control when testing multiple gene sets and genes. We illustrate the advantage of this procedure over procedures that only test gene sets or individual genes.
MOTIVATION: Microarray data analysis has expanded from testing individual genes for differential expression to testing gene sets for differential expression. The tests at the gene set level may focus on multivariate expression changes or on the differential expression of at least one gene in the gene set. These tests may be powerful at detecting subtle changes in expression, but findings at the gene set level need to be examined further to understand whether they are informative and if so how. RESULTS: We propose to first test for differential expression at the gene set level but then proceed to test for differential expression of individual genes within discovered gene sets. We introduce the overall false discovery rate (OFDR) as an appropriate error rate to control when testing multiple gene sets and genes. We illustrate the advantage of this procedure over procedures that only test gene sets or individual genes.
Authors: Eveline Pinseel; Teofil Nakov; Koen Van den Berge; Kala M Downey; Kathryn J Judy; Olga Kourtchenko; Anke Kremp; Elizabeth C Ruck; Conny Sjöqvist; Mats Töpel; Anna Godhe; Andrew J Alverson Journal: ISME J Date: 2022-04-05 Impact factor: 11.217
Authors: Sara Moeys; Johannes Frenkel; Christine Lembke; Jeroen T F Gillard; Valerie Devos; Koen Van den Berge; Barbara Bouillon; Marie J J Huysman; Sam De Decker; Julia Scharf; Atle Bones; Tore Brembu; Per Winge; Koen Sabbe; Marnik Vuylsteke; Lieven Clement; Lieven De Veylder; Georg Pohnert; Wim Vyverman Journal: Sci Rep Date: 2016-01-20 Impact factor: 4.379