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

Abstract

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.

Metabolomics meets systems immunology

“…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 ).…”