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This has led to the development of more refined analysis schemes, including physiological, behavioral, developmental and cytological tests. However, transcriptomic analyses have not yet been systematically evaluated for non-lethal knockouts. We conducted a power analysis to determine the experimental conditions under which even small changes in transcript levels can be reliably traced. We have applied this to two gene disruption lines of genes for which no function was known so far. Dedicated phenotyping tests informed by the tissues and stages of highest expression of the two genes show small effects on the tested phenotypes. For the transcriptome analysis of these stages and tissues, we used a prior power analysis to determine the number of biological replicates and the sequencing depth. We find that under these conditions, the knockouts have a significant impact on the transcriptional networks, with thousands of genes showing small transcriptional changes. GO analysis suggests that <jats:italic>A930004D18Rik<\/jats:italic> is involved in developmental processes through contributing to protein complexes, and <jats:italic>A830005F24Rik<\/jats:italic> in extracellular matrix functions. Subsampling analysis of the data reveals that the increase in the number of biological replicates was more important that increasing the sequencing depth to arrive at these results. Hence, our proof-of-principle experiment suggests that transcriptomic analysis is indeed an option to study gene functions of genes with weak or no traceable phenotypic effects and it provides the boundary conditions under which this is possible.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008354","type":"journal-article","created":{"date-parts":[[2020,11,12]],"date-time":"2020-11-12T18:53:00Z","timestamp":1605207180000},"page":"e1008354","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout 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