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 KoletiDusica Vidovic, Daniel J.B. Clarke, Stephan C. Schürer, Avi Ma’ayan, Jarek Meller, Mario Medvedovic

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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 (, 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.

Original languageEnglish
Article number4678
JournalNature Communications
Issue number1
StatePublished - Dec 2022


Dive into the research topics of 'Connecting omics signatures and revealing biological mechanisms with iLINCS'. Together they form a unique fingerprint.

Cite this