drug_target_interaction_example

Drug target interaction example data

datasets

Networks provide a means to incorporate molecular interactions into
reasoning, but on the omics-level, they are currently mainly used to combine
genomic and proteomic information. We here present a novel network analysis
pipeline that enables integrative analysis of multi-omics data including
metabolomics. It allows for comparative conclusions between two different
conditions, such as tumor subgroups, healthy vs. disease, or generally control
vs. perturbed.
Our approach focuses on interactions and their strength instead of on node
properties and includes molecules with low abundance and unknown function. We
use correlation-induced networks that are reduced and combined to form
heterogeneous, multi-omics molecular networks. Prior information such as
metabolite-protein interactions are incorporated. A semi-local, path-based
integration step denoises the network and ensures integrative conclusions. As
case studies, we investigate differential drug response in breast cancer tumor
datasets providing proteomics, transcriptomics, phospho-proteomics and
metabolomics data and contrasting patients with different estrogen receptor
status.
Our proposed pipeline leverages multi-omics data for differential predictions,
e.g. on drug response, and includes prior information on interactions.
The case study presented in the vignette uses data published by
Krug (2020) <doi:10.1016/j.cell.2020.10.036>. The package license applies only
to the software and explicitly not to the included data.

Katharina Baum

molnet

Predicting Differential Drug Response using Multi-Omics Networks

Julian Hugo

Spoorthi Kashyap

Nataniel M<c3><bc>ller

Justus Zeinert

drug_target_interaction_example function

A named list with 3 items.<dl class="dl-horizontal">
 <dt>target_molecules</dt><dd>Name of layer containing the drug targets. This name has to match the
 corresponding named item in the list of layers supplied to <code><a rd-options="" href="/link/start_pipeline?package=molnet&version=0.1.0" data-mini-rdoc="molnet::start_pipeline">start_pipeline</a></code>.</dd>
 <dt>interaction_table</dt><dd>Table giving drug-gene-interactions.</dd><dt>gene_name</dt><dd>Gene names of targeted protein-coding genes.</dd>
 <dt>ncbi_id</dt><dd>NCBI IDs of targeted protein-coding genes.</dd>
 <dt>drug_name</dt><dd>Drug-names with known interactions.</dd>
 <dt>drug_chembl_id</dt><dd>ChEMBL ID of drugs.</dd><dt>match_on</dt><dd>Column name of the data frame supplied in `interaction_table` that is used for
 matching drugs and target nodes in the graph (e.g. `ncbi_id`).</dd>
</dl>

Format

Drug target interaction example data — drug_target_interaction_example

Drug target interaction example data

drug_target_interaction_example: Drug target interaction example data

Description

Usage

Arguments

Format