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    Inferring causal molecular networks: empirical assessment through a community-based effort

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    Hill, Steven M.; Heiser, Laura M.; Cokelaer, Thomas; Unger, Michael; Nesser, Nicole K.; More... Carlin, Daniel E.; Zhang, Yang; Sokolov, Artem; Paull, Evan O.; Wong, Chris K.; Graim, Kiley; Bivol, Adrian; Wang, Haizhou; Zhu, Fan; Afsari, Bahman; Danilova, Ludmila V.; Favorov, Alexander V.; Lee, Wai Shing; Taylor, Dane; Hu, Chenyue W.; Long, Byron L.; Noren, David P.; Bisberg, Alexander J.; HPN-DREAM Consortium; Mills, Gordon B.; Gray, Joe W.; Kellen, Michael; Norman, Thea; Friend, Stephen; Qutub, Amina A.; Fertig, Elana J.; Guan, Yuanfang; Song, Mingzhou; Stuart, Joshua M.; Spellman, Paul T.; Koeppl, Heinz; Stolovitzky, Gustavo; Saez-Rodriguez, Julio; Mukherjee, Sach Less...
    Date
    2016
    Abstract
    It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well asᅠin silicoᅠdata from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense.
    Citation
    Hill, Steven M., Heiser, Laura M., Cokelaer, Thomas, et al.. "Inferring causal molecular networks: empirical assessment through a community-based effort." Nature Methods, 13, (2016) Springer Nature: 310-318. https://doi.org/10.1038/nmeth.3773.
    Published Version
    https://doi.org/10.1038/nmeth.3773
    Type
    Journal article
    Publisher
    Springer Nature
    Citable link to this page
    https://hdl.handle.net/1911/94203
    Rights
    This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material.ᅠ
    Link to License
    https://creativecommons.org/licenses/by-nc-sa/3.0/
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    • Bioengineering Publications [632]
    • Faculty Publications [4988]

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    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map