Dataset Information

DrDimont: explainable drug response prediction from differential analysis of multi-omics networks.

ABSTRACT:

Motivation

While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem.

Results

We present DrDimont, Drug response prediction from Differential analysis of multi-omics networks. It allows for comparative conclusions between two conditions and translates them into differential drug response predictions. DrDimont focuses on molecular interactions. It establishes condition-specific networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks. A novel semi-local, path-based integration step ensures integrative conclusions. Differential predictions are derived from comparing the condition-specific integrated networks. DrDimont's predictions are explainable, i.e. molecular differences that are the source of high differential drug scores can be retrieved. We predict differential drug response in breast cancer using transcriptomics, proteomics, phosphosite and metabolomics measurements and contrast estrogen receptor positive and receptor negative patients. DrDimont performs better than drug prediction based on differential protein expression or PageRank when evaluating it on ground truth data from cancer cell lines. We find proteomic and phosphosite layers to carry most information for distinguishing drug response.

Availability and implementation

DrDimont is available on CRAN: https://cran.r-project.org/package=DrDimont.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Hiort P

PROVIDER: S-EPMC9486584 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Publications

DrDimont: explainable drug response prediction from differential analysis of multi-omics networks.

Hiort Pauline P Hugo Julian J Zeinert Justus J Müller Nataniel N Kashyap Spoorthi S Rajapakse Jagath C JC Azuaje Francisco F Renard Bernhard Y BY Baum Katharina K

Bioinformatics (Oxford, England) 20220901 Suppl_2

<h4>Motivation</h4>While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem.<h4>Results</h4>We present DrDimont, Drug response prediction from Differen ...[more]

PMID: 36124784

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Dataset Information

DrDimont: explainable drug response prediction from differential analysis of multi-omics networks.

Motivation

Results

Availability and implementation

Supplementary information

Publications

DrDimont: explainable drug response prediction from differential analysis of multi-omics networks.

Similar Datasets

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