Connecting omics signatures and revealing biological mechanisms with iLINCS.

Autor: Pilarczyk M; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Fazel-Najafabadi M; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Kouril M; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA., Shamsaei B; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Vasiliauskas J; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Niu W; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Mahi N; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Zhang L; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Clark NA; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Ren Y; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., White S; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Karim R; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45220, USA., Xu H; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Biesiada J; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA., Bennett MF; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Davidson SE; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA., Reichard JF; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA., Roberts K; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA., Stathias V; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.; Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL 33136, USA., Koleti A; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.; Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL 33136, USA., Vidovic D; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.; Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL 33136, USA., Clarke DJB; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Schürer SC; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.; Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL 33136, USA., Ma'ayan A; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Meller J; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.; LINCS Data Coordination and Integration Center (DCIC), New York, USA.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.; Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45220, USA., Medvedovic M; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA. Medvedm@ucmail.uc.edu.; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA. Medvedm@ucmail.uc.edu.; LINCS Data Coordination and Integration Center (DCIC), New York, USA. Medvedm@ucmail.uc.edu.; LINCS Data Coordination and Integration Center (DCIC), Miami, USA. Medvedm@ucmail.uc.edu.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2022 Aug 09; Vol. 13 (1), pp. 4678. Date of Electronic Publication: 2022 Aug 09.
DOI: 10.1038/s41467-022-32205-3
Abstrakt: There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Here we present iLINCS ( http://ilincs.org ), an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The platform facilitates mining and re-analysis of the large collection of omics datasets (>34,000), pre-computed signatures (>200,000), and their connections, as well as the analysis of user-submitted omics signatures of diseases and cellular perturbations. iLINCS analysis workflows integrate vast omics data resources and a range of analytics and interactive visualization tools into a comprehensive platform for analysis of omics signatures. iLINCS user-friendly interfaces enable execution of sophisticated analyses of omics signatures, mechanism of action analysis, and signature-driven drug repositioning. We illustrate the utility of iLINCS with three use cases involving analysis of cancer proteogenomic signatures, COVID 19 transcriptomic signatures and mTOR signaling.
(© 2022. The Author(s).)
Databáze: MEDLINE
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