| |  Online-Ressource |
|---|
| Verfasst von: | White, Brian S. [VerfasserIn]  |
|---|
| | de Reyniès, Aurélien [VerfasserIn] |
|---|
| | Newman, Aaron M. [VerfasserIn] |
|---|
| | Waterfall, Joshua J. [VerfasserIn] |
|---|
| | Lamb, Andrew [VerfasserIn] |
|---|
| | Petitprez, Florent [VerfasserIn] |
|---|
| | Lin, Yating [VerfasserIn] |
|---|
| | Yu, Rongshan [VerfasserIn] |
|---|
| | Guerrero-Gimenez, Martin E. [VerfasserIn] |
|---|
| | Domanskyi, Sergii [VerfasserIn] |
|---|
| | Monaco, Gianni [VerfasserIn] |
|---|
| | Chung, Verena [VerfasserIn] |
|---|
| | Banerjee, Jineta [VerfasserIn] |
|---|
| | Derrick, Daniel [VerfasserIn] |
|---|
| | Valdeolivas, Alberto [VerfasserIn] |
|---|
| | Li, Haojun [VerfasserIn] |
|---|
| | Xiao, Xu [VerfasserIn] |
|---|
| | Wang, Shun [VerfasserIn] |
|---|
| | Zheng, Frank [VerfasserIn] |
|---|
| | Yang, Wenxian [VerfasserIn] |
|---|
| | Catania, Carlos A. [VerfasserIn] |
|---|
| | Lang, Benjamin J. [VerfasserIn] |
|---|
| | Bertus, Thomas J. [VerfasserIn] |
|---|
| | Piermarocchi, Carlo [VerfasserIn] |
|---|
| | Caruso, Francesca P. [VerfasserIn] |
|---|
| | Ceccarelli, Michele [VerfasserIn] |
|---|
| | Yu, Thomas [VerfasserIn] |
|---|
| | Guo, Xindi [VerfasserIn] |
|---|
| | Bletz, Julie [VerfasserIn] |
|---|
| | Coller, John [VerfasserIn] |
|---|
| | Maecker, Holden [VerfasserIn] |
|---|
| | Duault, Caroline [VerfasserIn] |
|---|
| | Shokoohi, Vida [VerfasserIn] |
|---|
| | Patel, Shailja [VerfasserIn] |
|---|
| | Liliental, Joanna E. [VerfasserIn] |
|---|
| | Simon, Stockard [VerfasserIn] |
|---|
| | Sáez Rodríguez, Julio [VerfasserIn] |
|---|
| | Heiser, Laura M. [VerfasserIn] |
|---|
| | Guinney, Justin [VerfasserIn] |
|---|
| | Gentles, Andrew J. [VerfasserIn] |
|---|
| Titel: | Community assessment of methods to deconvolve cellular composition from bulk gene expression |
|---|
| Verf.angabe: | Brian S. White, Aurélien de Reyniès, Aaron M. Newman, Joshua J. Waterfall, Andrew Lamb, Florent Petitprez, Yating Lin, Rongshan Yu, Martin E. Guerrero-Gimenez, Sergii Domanskyi, Gianni Monaco, Verena Chung, Jineta Banerjee, Daniel Derrick, Alberto Valdeolivas, Haojun Li, Xu Xiao, Shun Wang, Frank Zheng, Wenxian Yang, Carlos A. Catania, Benjamin J. Lang, Thomas J. Bertus, Carlo Piermarocchi, Francesca P. Caruso, Michele Ceccarelli, Thomas Yu, Xindi Guo, Julie Bletz, John Coller, Holden Maecker, Caroline Duault, Vida Shokoohi, Shailja Patel, Joanna E. Liliental, Stockard Simon, Julio Saez-Rodriguez, Laura M. Heiser, Justin Guinney & Andrew J. Gentles |
|---|
| E-Jahr: | 2024 |
|---|
| Jahr: | 27 August 2024 |
|---|
| Umfang: | 22 S. |
|---|
| Illustrationen: | Illustrationen |
|---|
| Fussnoten: | Gesehen am 14.03.2025 |
|---|
| Titel Quelle: | Enthalten in: Nature Communications |
|---|
| Ort Quelle: | [London] : Springer Nature, 2010 |
|---|
| Jahr Quelle: | 2024 |
|---|
| Band/Heft Quelle: | 15(2024), Artikel-ID 7362, Seite 1-22 |
|---|
| ISSN Quelle: | 2041-1723 |
|---|
| Abstract: | We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states. |
|---|
| DOI: | doi:10.1038/s41467-024-50618-0 |
|---|
| URL: | Bitte beachten Sie: Dies ist ein Bibliographieeintrag. Ein Volltextzugriff für Mitglieder der Universität besteht hier nur, falls für die entsprechende Zeitschrift/den entsprechenden Sammelband ein Abonnement besteht oder es sich um einen OpenAccess-Titel handelt.
kostenfrei: Volltext: https://doi.org/10.1038/s41467-024-50618-0 |
|---|
| | kostenfrei: Volltext: https://www.nature.com/articles/s41467-024-50618-0 |
|---|
| | DOI: https://doi.org/10.1038/s41467-024-50618-0 |
|---|
| Datenträger: | Online-Ressource |
|---|
| Sprache: | eng |
|---|
| Sach-SW: | Bioinformatics |
|---|
| | Cancer genomics |
|---|
| | Cancer microenvironment |
|---|
| | Computational models |
|---|
| | Immunology |
|---|
| K10plus-PPN: | 1919774092 |
|---|
| Verknüpfungen: | → Zeitschrift |
|---|
Community assessment of methods to deconvolve cellular composition from bulk gene expression / White, Brian S. [VerfasserIn]; 27 August 2024 (Online-Ressource)
