Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines

by Chen Xie, Cemalettin Bekpen, Sven K ünzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Skrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz Systematic knockout studies in mice have shown that a large fraction of the gene replacements show no lethal or other overt phenotypes. This has led to the development of more refined analysis schemes, including physiological, behavioral, developmental and cytological tests. However, transcriptomi c 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 f unction 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 biologica l 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 thatA930004D18Rik is involved in developmental processes through contributing to protein complexes, andA830005F24Rik in extracellular matrix functions. Subsampling analysis of the data reveals that the increase in ...
Source: PLoS Computational Biology - Category: Biology Authors: Source Type: research