Essay On Cell Morphology

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The main goal of this study is the development of a method to associate gene expression changes in response to perturbations with alterations in cell morphological features. The proposed approach for cell morphology enrichment analysis is composed of five main steps which we briefly describe here, illustrate in Figure 1, and discuss in detail in the rest of the Materials and Methods section.

\caption{Overview of the proposed approach for cell morphology enrichment analysis. The input data are collected from the LINCS database to yield database transcriptomic and cell morphological profiles in \textit{Step I}. In \textit{Step II}, we find
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Step V: Applications of method. A set of cell morphological gene sets and related transcriptomic profiles can be used to suit many applications, such as identification of gene-gene interactions, pathway analysis, and model to reveal most significant morphological changes in response to treatment with a compound.

\subsection{LINCS database}
The Library of Integrated Network-Based Cellular Signatures (LINCS) is a comprehensive public resource of gene expression signatures and other cellular processes in responses to a variety of perturbing agents, including 847 approved drugs and 30455 small compound molecules ($$). LINCS database is divided into the 11 category based on the biological processes, and 314 subcategories based on the type of experimental assays. The category of \textit{Cellular component organization} includes morphological features extracted from the cell-painting assay, representing changes in shape, texture, and intensity of major cellular components upon treatment with perturbing agents \cite{4}. Cell-painting assay is a fluorescence imaging multiplex cytological profiling assay that uses fluorescent dyes followed by automatic image in order to investigate the effects that compound treatments have on cells \cite{4}. LINCS project for \textit{Gene expression} profiling is divided to
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