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Connecting omics signatures and revealing biological mechanisms with iLINCS.
Pilarczyk, Marcin; Fazel-Najafabadi, Mehdi; Kouril, Michal; Shamsaei, Behrouz; Vasiliauskas, Juozas; Niu, Wen; Mahi, Naim; Zhang, Lixia; Clark, Nicholas A; Ren, Yan; White, Shana; Karim, Rashid; Xu, Huan; Biesiada, Jacek; Bennett, Mark F; Davidson, Sarah E; Reichard, John F; Roberts, Kurt; Stathias, Vasileios; Koleti, Amar; Vidovic, Dusica; Clarke, Daniel J B; Schürer, Stephan C; Ma'ayan, Avi; Meller, Jarek; Medvedovic, Mario.
  • Pilarczyk M; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.
  • Fazel-Najafabadi M; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.
  • Kouril M; LINCS Data Coordination and Integration Center (DCIC), New York, USA.
  • Shamsaei B; 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.
  • Niu W; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.
  • Mahi N; LINCS Data Coordination and Integration Center (DCIC), New York, USA.
  • Zhang L; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.
  • Clark NA; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.
  • Ren Y; LINCS Data Coordination and Integration Center (DCIC), New York, USA.
  • White S; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.
  • Karim R; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
  • Xu H; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.
  • Biesiada J; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.
  • Bennett MF; LINCS Data Coordination and Integration Center (DCIC), New York, USA.
  • Davidson SE; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.
  • Reichard JF; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.
  • Roberts K; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.
  • Stathias V; LINCS Data Coordination and Integration Center (DCIC), New York, USA.
  • Koleti A; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.
  • Vidovic D; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.
  • Clarke DJB; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.
  • Schürer SC; LINCS Data Coordination and Integration Center (DCIC), New York, USA.
  • Ma'ayan A; LINCS Data Coordination and Integration Center (DCIC), Miami, USA.
  • Meller J; Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.
  • Medvedovic M; LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.
Nat Commun ; 13(1): 4678, 2022 08 09.
Article in English | MEDLINE | ID: covidwho-1984385
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 / Neoplasms Limits: Humans Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-32205-3

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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 / Neoplasms Limits: Humans Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-32205-3