Connecting omics signatures and revealing biological mechanisms with iLINCS

Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Michal Kouril, Behrouz Shamsaei, Juozas Vasiliauskas, Wen Niu, Naim Mahi, Lixia Zhang, Nicholas A. Clark, Yan Ren, Shana White, Rashid Karim, Huan Xu, Jacek Biesiada, Mark F. Bennett, Sarah E. Davidson, John F. Reichard, Kurt Roberts, Vasileios Stathias, Amar Koleti, Dusica Vidovic, Daniel J. B. Clarke, Stephan C. Schürer, Avi Ma’ayan, Jarek Meller and Mario Medvedovic ()
Additional contact information
Marcin Pilarczyk: University of Cincinnati
Mehdi Fazel-Najafabadi: University of Cincinnati
Michal Kouril: LINCS Data Coordination and Integration Center (DCIC)
Behrouz Shamsaei: University of Cincinnati
Juozas Vasiliauskas: University of Cincinnati
Wen Niu: University of Cincinnati
Naim Mahi: University of Cincinnati
Lixia Zhang: University of Cincinnati
Nicholas A. Clark: University of Cincinnati
Yan Ren: University of Cincinnati
Shana White: University of Cincinnati
Rashid Karim: University of Cincinnati
Huan Xu: University of Cincinnati
Jacek Biesiada: University of Cincinnati
Mark F. Bennett: University of Cincinnati
Sarah E. Davidson: University of Cincinnati
John F. Reichard: University of Cincinnati
Kurt Roberts: University of Cincinnati
Vasileios Stathias: LINCS Data Coordination and Integration Center (DCIC)
Amar Koleti: LINCS Data Coordination and Integration Center (DCIC)
Dusica Vidovic: LINCS Data Coordination and Integration Center (DCIC)
Daniel J. B. Clarke: LINCS Data Coordination and Integration Center (DCIC)
Stephan C. Schürer: LINCS Data Coordination and Integration Center (DCIC)
Avi Ma’ayan: LINCS Data Coordination and Integration Center (DCIC)
Jarek Meller: University of Cincinnati
Mario Medvedovic: University of Cincinnati

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: 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.

Date: 2022
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32205-3

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DOI: 10.1038/s41467-022-32205-3

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