Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS

Marcin Pilarczyk, Michal Kouril, Behrouz Shamsaei, Juozas Vasiliauskas, Wen Niu, Naim Mahi, Lixia Zhang, Nicholas Clark, Yan Ren, Shana White, Rashid Karim, Huan Xu, Jacek Biesiada, View ORCID ProfileMark F. Bennett, Sarah Davidson, John F Reichard, Kurt Roberts, Vasileios Stathias, Amar Koleti, Dusica Vidovic, Daniel J.B. Clarke, Stephan C. Schurer, Avi Ma’ayan, Jarek Meller, View ORCID ProfileMario Medvedovic
doi: https://doi.org/10.1101/826271
Marcin Pilarczyk
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michal Kouril
2Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Behrouz Shamsaei
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Juozas Vasiliauskas
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wen Niu
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Naim Mahi
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lixia Zhang
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nicholas Clark
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yan Ren
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shana White
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rashid Karim
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
5Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Huan Xu
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jacek Biesiada
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mark F. Bennett
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mark F. Bennett
Sarah Davidson
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John F Reichard
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
7Division of Industrial Hygiene, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kurt Roberts
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vasileios Stathias
3Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL, USA
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Amar Koleti
3Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL, USA
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dusica Vidovic
3Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL, USA
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel J.B. Clarke
4Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Stephan C. Schurer
3Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL, USA
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Avi Ma’ayan
4Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jarek Meller
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
2Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mario Medvedovic
1Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220
6LINCS Data Coordination and Integration Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mario Medvedovic
  • For correspondence: medvedm@ucmail.uc.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

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. Among these, iLINCS is unique in scope and versatility of the data provided and the analytics facilitated. iLINCS (http://ilincs.org) is an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The platform facilitates analysis of user-submitted omics signatures of diseases and cellular perturbations in the context of a large compendium of pre-computed signatures (>200,000), as well as mining and re-analysis of the large collection of omics datasets (>12,000), pre-computed signatures, and their connections. Analytics workflows driven by user-friendly interfaces enable users with only conceptual understanding of the analysis strategy to execute sophisticated analyses of omics signatures, such as systems biology analyses and interpretation of signatures, mechanism of action analysis, and signature-driven drug repositioning. In summary, iLINCS workflows integrate vast omics data resources and a range of analytics and interactive visualization tools into a comprehensive platform for analysis of omics signatures.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Methods section has been updated. Additional use cases have been referenced. Results of a benchmark comparisons for choosing the connectivity metric have been added. A table outlining differences with selected other resources has been added.

  • http://ilincs.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted November 08, 2020.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS
Marcin Pilarczyk, Michal Kouril, Behrouz Shamsaei, Juozas Vasiliauskas, Wen Niu, Naim Mahi, Lixia Zhang, Nicholas Clark, Yan Ren, Shana White, Rashid Karim, Huan Xu, Jacek Biesiada, Mark F. Bennett, Sarah Davidson, John F Reichard, Kurt Roberts, Vasileios Stathias, Amar Koleti, Dusica Vidovic, Daniel J.B. Clarke, Stephan C. Schurer, Avi Ma’ayan, Jarek Meller, Mario Medvedovic
bioRxiv 826271; doi: https://doi.org/10.1101/826271
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS
Marcin Pilarczyk, Michal Kouril, Behrouz Shamsaei, Juozas Vasiliauskas, Wen Niu, Naim Mahi, Lixia Zhang, Nicholas Clark, Yan Ren, Shana White, Rashid Karim, Huan Xu, Jacek Biesiada, Mark F. Bennett, Sarah Davidson, John F Reichard, Kurt Roberts, Vasileios Stathias, Amar Koleti, Dusica Vidovic, Daniel J.B. Clarke, Stephan C. Schurer, Avi Ma’ayan, Jarek Meller, Mario Medvedovic
bioRxiv 826271; doi: https://doi.org/10.1101/826271

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3691)
  • Biochemistry (7800)
  • Bioengineering (5678)
  • Bioinformatics (21295)
  • Biophysics (10584)
  • Cancer Biology (8179)
  • Cell Biology (11948)
  • Clinical Trials (138)
  • Developmental Biology (6764)
  • Ecology (10401)
  • Epidemiology (2065)
  • Evolutionary Biology (13875)
  • Genetics (9709)
  • Genomics (13075)
  • Immunology (8151)
  • Microbiology (20022)
  • Molecular Biology (7859)
  • Neuroscience (43073)
  • Paleontology (321)
  • Pathology (1279)
  • Pharmacology and Toxicology (2261)
  • Physiology (3353)
  • Plant Biology (7232)
  • Scientific Communication and Education (1314)
  • Synthetic Biology (2008)
  • Systems Biology (5539)
  • Zoology (1128)