Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation

Han Jin; Cheng Zhang; Martin Zwahlen; Kalle von Feilitzen; Max Karlsson; Mengnan Shi; Meng Yuan; Xiya Song; Xiangyu Li; Hong Yang; Hasan Turkez; Linn Fagerberg; Mathias Uhlén; Adil Mardinoglu

doi:10.1038/s41467-023-41132-w

Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation

Han Jin, Cheng Zhang, Martin Zwahlen, Kalle von Feilitzen, Max Karlsson, Mengnan Shi, Meng Yuan, Xiya Song, Xiangyu Li, Hong Yang, Hasan Turkez, Linn Fagerberg, Mathias Uhlén^*, Adil Mardinoglu^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

Cell lines are valuable resources as model for human biology and translational medicine. It is thus important to explore the concordance between the expression in various cell lines vis-à-vis human native and disease tissues. In this study, we investigate the expression of all human protein-coding genes in more than 1,000 human cell lines representing 27 cancer types by a genome-wide transcriptomics analysis. The cell line gene expression is compared with the corresponding profiles in various tissues, organs, single-cell types and cancers. Here, we present the expression for each cell line and give guidance for the most appropriate cell line for a given experimental study. In addition, we explore the cancer-related pathway and cytokine activity of the cell lines to aid human biology studies and drug development projects. All data are presented in an open access cell line section of the Human Protein Atlas to facilitate the exploration of all human protein-coding genes across these cell lines.

Original language	English
Article number	5417
Journal	Nature Communications
Volume	14
Issue number	1
Early online date	5 Sept 2023
DOIs	https://doi.org/10.1038/s41467-023-41132-w
Publication status	Published - Dec 2023

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10.1038/s41467-023-41132-wLicence: CC BY

Systematic transcriptional analysis of_JIN_Publishedonline5September2023_GOLD_VoR (CC BY)Final published version, 4.18 MBLicence: CC BY

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Jin, H., Zhang, C., Zwahlen, M., von Feilitzen, K., Karlsson, M., Shi, M., Yuan, M., Song, X., Li, X., Yang, H., Turkez, H., Fagerberg, L., Uhlén, M., & Mardinoglu, A. (2023). Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation. Nature Communications, 14(1), Article 5417. https://doi.org/10.1038/s41467-023-41132-w

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abstract = "Cell lines are valuable resources as model for human biology and translational medicine. It is thus important to explore the concordance between the expression in various cell lines vis-{\`a}-vis human native and disease tissues. In this study, we investigate the expression of all human protein-coding genes in more than 1,000 human cell lines representing 27 cancer types by a genome-wide transcriptomics analysis. The cell line gene expression is compared with the corresponding profiles in various tissues, organs, single-cell types and cancers. Here, we present the expression for each cell line and give guidance for the most appropriate cell line for a given experimental study. In addition, we explore the cancer-related pathway and cytokine activity of the cell lines to aid human biology studies and drug development projects. All data are presented in an open access cell line section of the Human Protein Atlas to facilitate the exploration of all human protein-coding genes across these cell lines.",

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AU - Jin, Han

AU - Zhang, Cheng

AU - Zwahlen, Martin

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AU - Karlsson, Max

AU - Shi, Mengnan

AU - Yuan, Meng

AU - Song, Xiya

AU - Li, Xiangyu

AU - Yang, Hong

AU - Turkez, Hasan

AU - Fagerberg, Linn

AU - Uhlén, Mathias

AU - Mardinoglu, Adil

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AB - Cell lines are valuable resources as model for human biology and translational medicine. It is thus important to explore the concordance between the expression in various cell lines vis-à-vis human native and disease tissues. In this study, we investigate the expression of all human protein-coding genes in more than 1,000 human cell lines representing 27 cancer types by a genome-wide transcriptomics analysis. The cell line gene expression is compared with the corresponding profiles in various tissues, organs, single-cell types and cancers. Here, we present the expression for each cell line and give guidance for the most appropriate cell line for a given experimental study. In addition, we explore the cancer-related pathway and cytokine activity of the cell lines to aid human biology studies and drug development projects. All data are presented in an open access cell line section of the Human Protein Atlas to facilitate the exploration of all human protein-coding genes across these cell lines.

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Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation

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