multiSLIDE is a web server for exploring connected elements of biological pathways in multi-omics data

Ghosh, Soumita; Datta, Abhik; Choi, Hyungwon

doi:10.1038/s41467-021-22650-x

Cited by 15 publications

(9 citation statements)

References 65 publications

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“…R packages for this strategy include MOFA (Argelaguet et al , 2018 ), mixOmics (Rohart et al , 2017 ), mixKernel (Mariette & Villa‐Vialaneix, 2018 ), and MoSBi (Rose et al , 2022 ). Web servers for this strategy include MAINE (Gruca et al , 2021 ), MultiSLIDE (Ghosh et al , 2021 ), Mergeomics (Ding et al , 2021a ), and SUMMER (Huang et al , 2020 ).…”

Section: Integrative Metabolomics In Immunology Researchmentioning

confidence: 99%

Metabolomics meets systems immunology

Zhu

et al. 2023

EMBO Reports

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Metabolic processes play a critical role in immune regulation. Metabolomics is the systematic analysis of small molecules (metabolites) in organisms or biological samples, providing an opportunity to comprehensively study interactions between metabolism and immunity in physiology and disease. Integrating metabolomics into systems immunology allows the exploration of the interactions of multilayered features in the biological system and the molecular regulatory mechanism of these features. Here, we provide an overview on recent technological developments of metabolomic applications in immunological research. To begin, two widely used metabolomics approaches are compared: targeted and untargeted metabolomics. Then, we provide a comprehensive overview of the analysis workflow and the computational tools available, including sample preparation, raw spectra data preprocessing, data processing, statistical analysis, and interpretation. Third, we describe how to integrate metabolomics with other omics approaches in immunological studies using available tools. Finally, we discuss new developments in metabolomics and its prospects for immunology research. This review provides guidance to researchers using metabolomics and multiomics in immunity research, thus facilitating the application of systems immunology to disease research.

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Section: Integrative Metabolomics In Immunology Researchmentioning

confidence: 99%

Metabolomics meets systems immunology

Zhu

et al. 2023

EMBO Reports

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“…Unfortunately, networks are frequently too large and interpretability is limited by the lack of context. A recent novel related method is multiSlide, which visualizes interconnected molecular features in heatmaps of multi-omics data sets ( 22 ).…”

Section: Introductionmentioning

confidence: 99%

PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases

Liu

Salguero

Petek

et al. 2022

Nucleic Acids Research

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PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology. PaintOmics 4 is available at https://paintomics.org/.

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“…The example of a web-based platform for multi-omics data analysis is PaintOmics 3 ( Hernández-de Diego et al , 2018 ) that provides the user with the methods for feature matching, pathway enrichment analysis and pathway-based results visualization. MultiSLIDE ( Ghosh et al , 2021 ) is a web-based interactive tool that allows to identify molecular signatures by statistical analysis and simultaneous visualization of molecular features in heatmaps of multi-omics datasets. MiBiOmics ( Zoppi et al , 2021 ) is another example of a web-based application for multi-omics data filtration, normalization and transformation.…”

Section: Introductionmentioning

confidence: 99%

MAINE: a web tool for multi-omics feature selection and rule-based data exploration

et al. 2021

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Summary Patinent multi-omics datasets are often characterized by a high dimensionality, however usually only for a small fraction of the features is informative, that is changes in their values is directly related to the disease outcome or patient survival. In medical sciences, in addition to a robust feature selection procedure, the ability to discover human-readable patterns in the analysed data is also desirable. To address this need, we created MAINE—Multi-omics Analysis and Exploration. The unique functionality of MAINE is the ability to discover multidimensional dependencies between the selected multi-omics features and event outcome prediction as well as patient survival probability. Learned patterns are visualized in the form of interpretable decision/survival trees and rules. Availability MAINE is freely available at maine.ibemag.pl as an online web application. Supplementary information Supplementary data are available at Bioinformatics online.

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multiSLIDE is a web server for exploring connected elements of biological pathways in multi-omics data

Cited by 15 publications

References 65 publications

Metabolomics meets systems immunology

Metabolomics meets systems immunology

PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases

MAINE: a web tool for multi-omics feature selection and rule-based data exploration

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