TY - JOUR
T1 - Connecting omics signatures and revealing biological mechanisms with iLINCS
AU - Pilarczyk, Marcin
AU - Fazel-Najafabadi, Mehdi
AU - Kouril, Michal
AU - Shamsaei, Behrouz
AU - Vasiliauskas, Juozas
AU - Niu, Wen
AU - Mahi, Naim
AU - Zhang, Lixia
AU - Clark, Nicholas A.
AU - Ren, Yan
AU - White, Shana
AU - Karim, Rashid
AU - Xu, Huan
AU - Biesiada, Jacek
AU - Bennett, Mark F.
AU - Davidson, Sarah E.
AU - Reichard, John F.
AU - Roberts, Kurt
AU - Stathias, Vasileios
AU - Koleti, Amar
AU - Vidovic, Dusica
AU - Clarke, Daniel J.B.
AU - Schürer, Stephan C.
AU - Ma’ayan, Avi
AU - Meller, Jarek
AU - Medvedovic, Mario
N1 - Funding Information:
We would like acknowledge helpful comments about the manuscript provided by Dr. Albert Lee and Dr. Ajay Pillai. We would also like to acknowledge the contributions of Dr. Vineet Joshi and Dr. Mukta Phatak to the development of early prototypes of the iLINCS portal. The development of iLINCS was funded by the LINCS-BD2K Data Coordination and Integration Center U54 grant: U54HL127624 (A.M., M.M., and S.S.), Center for Environmental Genetics Bioinformatics Core: P30ES006096 (M.M.), and the Computational Tool Development and Integrative Data Analysis for LINCS U01 grant: U01HL111638 (M.M.).
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85135732373&partnerID=8YFLogxK
U2 - 10.1038/s41467-022-32205-3
DO - 10.1038/s41467-022-32205-3
M3 - Article
C2 - 35945222
AN - SCOPUS:85135732373
SN - 2041-1723
VL - 13
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 4678
ER -