MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis

Alexandre Maes; Xavier Martinez; Karen Druart; Benoist Laurent; Sean Guégan; Christophe H Marchand; Stéphane D Lemaire; Marc Baaden

doi:10.1515/jib-2018-0006

MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis

J Integr Bioinform. 2018 Jun 21;15(2):20180006. doi: 10.1515/jib-2018-0006.

Authors

Alexandre Maes¹, Xavier Martinez², Karen Druart², Benoist Laurent³, Sean Guégan², Christophe H Marchand¹, Stéphane D Lemaire¹, Marc Baaden²

Affiliations

¹ Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, 13 rue Pierre et Marie Curie, 75005, Paris, France.
² Laboratoire de Biochimie Théorique, CNRS, UPR9080, Institut de Biologie Physico-Chimique, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005, Paris, France.
³ Institut de Biologie Physico-Chimique, FRC 550, CNRS, Paris, France.

Abstract

Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins. We aim to understand underlying molecular mechanisms and structural determinants through integration of redox proteome data from gene- to structural level. Our interactive visual analytics approach on an 8.3 m2 display wall of 25 MPixel resolution features stereoscopic three dimensions (3D) representation performed by UnityMol WebGL. Virtual reality headsets complement the range of usage configurations for fully immersive tasks. Our experiments confirm that fast access to a rich cross-linked database is necessary for immersive analysis of structural data. We emphasize the possibility to display complex data structures and relationships in 3D, intrinsic to molecular structure visualization, but less common for omics-network analysis. Our setup is powered by MinOmics, an integrated analysis pipeline and visualization framework dedicated to multi-omics analysis. MinOmics integrates data from various sources into a materialized physical repository. We evaluate its performance, a design criterion for the framework.

Keywords: Database; Display wall; Omics; Protein and proteome; Virtual Reality (VR).

MeSH terms

Algal Proteins / chemistry
Algal Proteins / metabolism*
Chlamydomonas reinhardtii / chemistry
Chlamydomonas reinhardtii / metabolism*
Computer Graphics*
Imaging, Three-Dimensional
Models, Structural
Oxidation-Reduction
Protein Conformation
Protein Interaction Maps
Protein Processing, Post-Translational*
Proteome / analysis
Proteomics / methods
Software*
Virtual Reality

Substances

Algal Proteins
Proteome

Grants and funding

This work was supported by the Paris Ile-de-France Region and by the Fondation pour la Recherche Médicale, grant number FRM DBI20141231801, to SL. XM and MB thank UCB Biopharma for support. We further acknowledge support by the “Initiative d’Excellence” program from the French State (Funder Id: 10.13039/501100001665, Grant “DYNAMO”, ANR-11-LABX-0011-01 and Funder Id: 10.13039/501100001665, Grant “CACSICE”, ANR-11-EQPX-0008)”.