iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments

Analytical Chemistry, vol. 97, pp. 2689–2697

Abstract

Abstract Omics technologies including genomics, proteomics, metabolomics, and lipidomics allow profound insights into health and disease. Thanks to plummeting costs of continuously evolving omics analytical platforms, research centers collect multi-omics data more routinely. They are, however, confronted with the lack of a versatile software solution to harmoniously analyze single-omics data and merge and interpret multi-omics data. We have developed iSODA, an interactive web-based application for the analysis of single-as well as multi-omics omics data. The software tool emphasizes intuitive, interactive visualizations designed for user-driven data exploration. Researchers can filter and normalize their datasets and access a variety of functions ranging from simple data visualization like volcano plots and PCA, to advanced functional analyses like enrichment analysis for proteomics and saturation analysis for lipidomics. For insights from integrated multi-omics, iSODA incorporates Multi-Omics Factor Analysis – MOFA, and Similarity Network Fusion – SNF. All results are presented in interactive plots with the possibility of downloading plots and associated data. The ability to adapt the imported data on-the-fly allows for tasks such as removal of outlier samples or failed features, various imputation strategies, or data normalization. The modular design allows for extensions with new analyses and plots. The software is accessible under http://isoda.online/ . Abstract Figure Graphical summary for iSODA showcasing some application examples, the data import, the single-omics and multi-omics modules.

Authors 11

1. Damien Olivier‐Jimenez Aachen Center for Proteomics and Metabolomics

   Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics and Metabolomics

   Leiden University Medical Center

   Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands

2. Rico J. E. Derks Aachen Center for Proteomics and Metabolomics

   Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics and Metabolomics

   Leiden University Medical Center

   Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands

3. Oscar Harari

   The Ohio State University

   Affiliation as printed

   Department of Neurology

   The Ohio State University

   Department of Neurology, The Ohio State University, Columbus, Ohio 43210, United States of America

4. Carlos C Cruchaga

   Washington University in St. Louis

   Affiliation as printed

   Washington University School of Medicine in St. Louis

   Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States of America

5. Muhammad Ali

   Washington University in St. Louis

   Affiliation as printed

   Washington University School of Medicine in St. Louis

   Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States of America

6. Alessandro Ori‬‬

   Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

   Affiliation as printed

   Leibniz Institute on Aging─Fritz Lipmann Institute (FLI)

7. Domenico Di Fraia

   Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

   Affiliation as printed

   Leibniz Institute on Aging─Fritz Lipmann Institute (FLI)

8. Birol Cabukusta Aachen Department of Cell and Chemical Biology Oncode Institute

   Leiden University Medical Center · Oncode Institute

   Affiliation as printed

   Department of Cell and Chemical Biology, ONCODE Institute

   Leiden University Medical Center

   Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden 2333ZA, Netherlands

9. Andy Henrie

   Data Tecnica International (United States)

   Affiliation as printed

   DataTecnica

   DataTecnica, Washington, District of Columbia 20037, United States of America

10. Martin A. Giera Aachen Center for Proteomics and Metabolomics

    Leiden University Medical Center

    Affiliation as printed

    Center for Proteomics and Metabolomics

    Leiden University Medical Center

    Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands

11. Yassene Mohammed corresponding Aachen Center for Proteomics and Metabolomics

    Leiden University Medical Center · McGill University

    Affiliation as printed

    Center for Proteomics and Metabolomics

    Gerald Bronfman Department of Oncology

    Leiden University Medical Center

    McGill University

    Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands

    Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec H3A 0G4, Canada