Context-specificity in causal signaling networks revealed by phosphoprotein profiling
Steven M. Hill,
Nicole K. Nesser,
Simon E.F. Spencer,
Laura M. Heiser,
Nupur T. Pande,
James E. Korkola,
Joe W. Gray,
Gordon B. Mills,
Paul T. Spellman
Posted 15 Feb 2016
bioRxiv DOI: 10.1101/039636 (published DOI: 10.1016/j.cels.2016.11.013)
Posted 15 Feb 2016
Signaling networks downstream of receptor tyrosine kinases are among the most extensively studied biological networks. However, it remains unclear whether signaling networks depend on biological context. Signaling networks encode causal influences - and not just correlations - between network components. Here, using a causal framework and systematic time-course assays of signaling proteins, we investigate the context-specificity of signaling networks in a cell line system. We focus on a well-defined set of signaling proteins profiled in four breast cancer cell lines under eight stimulus conditions and inhibition of specific kinases. The data, spanning multiple pathways and comprising approximately 70,000 phosphoprotein and 260,000 protein measurements, provide a wealth of testable, context-specific hypotheses, several of which we validate in independent experiments. Furthermore, the data provide a resource for computational methods development, permitting empirical assessment of causal network learning in a complex, mammalian setting.
- Downloaded 555 times
- Download rankings, all-time:
- Site-wide: 27,366 out of 89,036
- In systems biology: 780 out of 2,307
- Year to date:
- Site-wide: 84,081 out of 89,036
- Since beginning of last month:
- Site-wide: 78,538 out of 89,036
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!