دورية أكاديمية
Wisdom of crowds for robust gene network inference
| العنوان: | Wisdom of crowds for robust gene network inference |
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| المؤلفون: | Daniel Marbach, James C. Costello, Robert Küffner, Nicole M. Vega, Robert J. Prill, Diogo M. Camacho, Kyle R. Allison, Andrej Aderhold, Richard Bonneau, Yukun Chen, James J. Collins, Francesca Cordero, Martin Crane, Frank Dondelinger, Mathias Drton, Roberto Esposito, Rina Foygel, Alberto de la Fuente, Jan Gertheiss, Pierre Geurts, Alex Greenfield, Marco Grzegorczyk, Anne Claire Haury, Benjamin Holmes, Torsten Hothorn, Dirk Husmeier, Vân Anh Huynh Thu, Alexandre Irrthum, Manolis Kellis, Guy Karlebach, Sophie Lèbre, Vincenzo De Leo, Aviv Madar, Subramani Mani, Fantine Mordelet, Harry Ostrer, Zhengyu Ouyang, Ravi Pandya, Tobias Petri, Andrea Pinna, Christopher S. Poultney, Serena Rezny, Heather J. Ruskin, Yvan Saeys, Ron Shamir, Mingzhou Song, Nicola Soranzo, Alexander Statnikov, Gustavo Stolovitzky, Nicci Vega, Paola Vera Licona, Jean Philippe Vert, Alessia Visconti, Haizhou Wang, Louis Wehenkel, Lukas Windhager, Yang Zhang, Ralf Zimmer, SIRBU, ALINA |
| المساهمون: | Daniel, Marbach, James C., Costello, Robert, Küffner, Nicole M., Vega, Robert J., Prill, Diogo M., Camacho, Kyle R., Allison, Andrej, Aderhold, Richard, Bonneau, Yukun, Chen, James J., Collin, Francesca, Cordero, Martin, Crane, Frank, Dondelinger, Mathias, Drton, Roberto, Esposito, Rina, Foygel, Alberto de la, Fuente, Jan, Gerthei, Pierre, Geurt, Alex, Greenfield, Marco, Grzegorczyk, Anne Claire, Haury, Benjamin, Holme, Torsten, Hothorn, Dirk, Husmeier, Vân Anh Huynh, Thu, Alexandre, Irrthum, Manolis, Kelli, Guy, Karlebach, Sophie, Lèbre, Vincenzo De, Leo, Aviv, Madar, Subramani, Mani, Fantine, Mordelet, Harry, Ostrer, Zhengyu, Ouyang, Ravi, Pandya, Tobias, Petri, Andrea, Pinna, Christopher S., Poultney, Serena, Rezny, Heather J., Ruskin, Yvan, Saey, Ron, Shamir, Sirbu, Alina, Mingzhou, Song, Nicola, Soranzo, Alexander, Statnikov, Gustavo, Stolovitzky, Nicci, Vega, Paola Vera, Licona, Jean Philippe, Vert, Alessia, Visconti, Haizhou, Wang, Louis, Wehenkel, Lukas, Windhager, Yang, Zhang, Ralf, Zimmer |
| سنة النشر: | 2012 |
| المجموعة: | ARPI - Archivio della Ricerca dell'Università di Pisa |
| مصطلحات موضوعية: | gene regulatory network, reverse engineering, integration |
| الوصف: | Reconstructing gene regulatory networks from high-throughput data is a long-standing challenge. Through the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, we performed a comprehensive blind assessment of over 30 network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae and in silico microarray data. We characterize the performance, data requirements and inherent biases of different inference approaches, and we provide guidelines for algorithm application and development. We observed that no single inference method performs optimally across all data sets. In contrast, integration of predictions from multiple inference methods shows robust and high performance across diverse data sets. We thereby constructed high-confidence networks for E. coli and S. aureus, each comprising ~1,700 transcriptional interactions at a precision of ~50%. We experimentally tested 53 previously unobserved regulatory interactions in E. coli, of which 23 (43%) were supported. Our results establish community-based methods as a powerful and robust tool for the inference of transcriptional gene regulatory networks. |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | STAMPA |
| اللغة: | English |
| العلاقة: | info:eu-repo/semantics/altIdentifier/pmid/22796662; info:eu-repo/semantics/altIdentifier/wos/WOS:000307015700019; volume:9; issue:8; firstpage:796; lastpage:804; numberofpages:8; journal:NATURE METHODS; http://hdl.handle.net/11568/773221Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84870305264; http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2016.htmlTest |
| DOI: | 10.1038/nmeth.2016 |
| الإتاحة: | https://doi.org/10.1038/nmeth.2016Test http://hdl.handle.net/11568/773221Test http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2016.htmlTest |
| رقم الانضمام: | edsbas.DC233329 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1038/nmeth.2016 |
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