Predicting the effects of cultivation condition on gene regulation in Escherichia coli by using deep learning.

ABSTRACT: Cell's physiology is affected by cultivation conditions at varying degrees, including carbon sources and inorganic nutrients in growth medium, and the presence or absence of aeration. When examining the effects of cultivation conditions on the cell, the cell's transcriptional response is often examined first among other phenotypes (e.g., proteome and metabolome). In this regard, we developed DeepMGR, a deep learning model that predicts the effects of culture media on gene regulation in Escherichia coli. DeepMGR specifically classifies the direction of gene regulation (i.e., upregulation, no regulation, or downregulation) for an input gene in comparison with M9 minimal medium with glucose as a control condition. For this classification task, DeepMGR uses a feedfo

SUBMITTER: Kwon MS 

PROVIDER: S-EPMC10781998 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature