Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
STAR Protoc. 2021 Jan 22;2(1):100280. doi: 10.1016/j.xpro.2020.100280. eCollection 2021 Mar 19.
Targeted identification of cellular processes responsible for a phenotype is of major importance in guiding efforts in bioengineering and medicine. Genome-scale metabolic models (GEMs) are widely used to integrate various types of omics data and study the cellular physiology under different conditions. Here, we present PhenoMapping, a protocol that uses GEMs, omics, and phenotypic data to map cellular processes and observed phenotypes. PhenoMapping also classifies genes as conditionally and unconditionally essential and guides a comprehensive curation of GEMs. For complete details on the use and execution of this protocol, please refer to Stanway et al. (2019) and Krishnan et al. (2020).
靶向鉴定负责表型的细胞过程对于指导生物工程和医学领域的研究工作至关重要。基因组规模代谢模型（GEM）被广泛用于整合各种类型的组学数据，并在不同条件下研究细胞生理学。在这里，我们提出了 PhenoMapping 方法，该方法使用 GEM、组学和表型数据来映射细胞过程和观察到的表型。PhenoMapping 还将基因分类为条件必需和非条件必需，并指导对 GEM 的全面整理。有关该协议的使用和执行的完整详细信息，请参阅 Stanway 等人（2019 年）和 Krishnan 等人（2020 年）。
