Fig. 2: Overview of the workflow employed in this study. | Communications Biology

Fig. 2: Overview of the workflow employed in this study.

From: Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection

Fig. 2

L1000 technology for Gene Expression and Cell Painting Technology for cell morphology statistics. The LINCS L1000 gene expression technology profiles changes in 978 landmark genes before and after chemical perturbations on different human cell lines. Raw unprocessed flow cytometry data from Luminex is converted to quantile-normalized gene expression profiles for all replicates of each compound. We use Gene Expression data from Wang et al.45, who for each compound, computed the strongest gene expression signature using the Characteristic Direction (CD) method and computed enrichment p values for each CD signature in the space of all genes against gene set libraries using Principal Angle Enrichment Analysis (PAEA). The Cell Painting assay, on the other hand, captures cellular morphological changes in the form of numerical statistics which are converted from microscopic image data of cells treated with chemical perturbations. The Figure was partly generated using Servier Medical Art, provided by Servier, licensed under a Creative Commons Attribution 3.0 unported license.

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