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; Mario Medvedovic

doi:10.1038/s41467-022-32205-3

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, Mario Medvedovic

Research output: Contribution to journal › Article › peer-review

86 Scopus citations

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.

Original language	English
Article number	4678
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-32205-3
State	Published - Dec 2022

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Pilarczyk, M., Fazel-Najafabadi, M., Kouril, M., Shamsaei, B., Vasiliauskas, J., Niu, W., Mahi, N., Zhang, L., Clark, N. A., Ren, Y., White, S., Karim, R., Xu, H., Biesiada, J., Bennett, M. F., Davidson, S. E., Reichard, J. F., Roberts, K., Stathias, V., ... Medvedovic, M. (2022). Connecting omics signatures and revealing biological mechanisms with iLINCS. Nature Communications , 13(1), Article 4678. https://doi.org/10.1038/s41467-022-32205-3

@article{e48a19a59c3e48578fc16987b38610ba,

title = "Connecting omics signatures and revealing biological mechanisms with iLINCS",

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.",

author = "Marcin Pilarczyk and Mehdi Fazel-Najafabadi and Michal Kouril and Behrouz Shamsaei and Juozas Vasiliauskas and Wen Niu and Naim Mahi and Lixia Zhang and Clark, \{Nicholas A.\} and Yan Ren and Shana White and Rashid Karim and Huan Xu and Jacek Biesiada and Bennett, \{Mark F.\} and Davidson, \{Sarah E.\} and Reichard, \{John F.\} and Kurt Roberts and Vasileios Stathias and Amar Koleti and Dusica Vidovic and Clarke, \{Daniel J.B.\} and Sch{\"u}rer, \{Stephan C.\} and Avi Ma{\textquoteright}ayan and Jarek Meller and Mario Medvedovic",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1038/s41467-022-32205-3",

language = "English",

volume = "13",

journal = "Nature Communications ",

issn = "2041-1723",

number = "1",

}

Pilarczyk, M, Fazel-Najafabadi, M, Kouril, M, Shamsaei, B, Vasiliauskas, J, Niu, W, Mahi, N, Zhang, L, Clark, NA, Ren, Y, White, S, Karim, R, Xu, H, Biesiada, J, Bennett, MF, Davidson, SE, Reichard, JF, Roberts, K, Stathias, V, Koleti, A, Vidovic, D, Clarke, DJB, Schürer, SC, Ma’ayan, A, Meller, J & Medvedovic, M 2022, 'Connecting omics signatures and revealing biological mechanisms with iLINCS', Nature Communications , vol. 13, no. 1, 4678. https://doi.org/10.1038/s41467-022-32205-3

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

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 - https://www.scopus.com/pages/publications/85135732373

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 -

Connecting omics signatures and revealing biological mechanisms with iLINCS

Abstract

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