phosphoprotein_data

Phosphosite analysis of breast cancer patients data from Krug et al., 2020 (data from the
Clinical Proteomic Tumor Analysis Consortium (CPTAC)). The data is stratified by estrogen
receptor (ER) expression status (group1 = ER+, group2 = ER-). Each group is given as a sub-list
containing 'data' (raw data, phosphosites in columns and samples in rows) and 'identifiers'
(one column per identifier, rows in the same order as the phosphosite order in '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

phosphoprotein_data function

<dl class="dl-horizontal">
 <dt>group1</dt><dd>ER+ data</dd><dt>data</dt><dd>raw data, phosphosites in columns and samples in rows</dd>
 <dt>identifiers</dt><dd>one column per identifier, rows in the same order as the phoshosite order
 in 'data', identifiers: Phosphosite ID, RefSeq ID, gene name</dd><dt>group2</dt><dd>ER- data</dd><dt>data</dt><dd>see above</dd>
 <dt>identifiers</dt><dd>see above</dd></dl>

Format

Phosphosite data — phosphoprotein_data

Phosphosite data

phosphoprotein_data: Phosphosite data

Description

Usage

Arguments

Format