Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements.

ABSTRACT: RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes with HIF-1-dependent expression that have opposite changes in expression in mutants of two ge

SUBMITTER: Angeles-Albores D 

PROVIDER: S-EPMC5879656 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature