Instruct: Identify the main category of Biorxiv papers based on the titles and abstracts
Query: Motif-based phosphoproteome clustering improves modeling and interpretation Cell signaling is orchestrated in part through a network of protein kinases and phosphatases. Dysregulation of kinase signaling is widespread in diseases such as cancer and is readily targetable through inhibitors of kinase enzymatic activity. Mass spectrometry-based analysis of kinase signaling can provide a global view of kinase signaling regulation but making sense of these data is complicated by its stochastic coverage of the proteome, measurement of substrates rather than kinase signaling itself, and the scale of the data collected. Here, we implement a dual data and motif clustering strategy (DDMC) that simultaneously clusters substrate peptides into similarly regulated groups based on their variation within an experiment and their sequence profile. We show that this can help to identify putative upstream kinases and supply more robust clustering. We apply this clustering to large-scale clinical proteomic profiling of lung cancer and identify conserved proteomic signatures of tumorigenicity, genetic mutations, and tumor immune infiltration. We propose that DDMC provides a general and flexible clustering strategy for the analysis of phosphoproteomic data.

One-sentence SummaryDDMC is a general and flexible strategy for phosphoproteomic analysis by clustering phosphopeptides using both their phosphorylation abundance and sequence motifs.
23
The categories of this paper are: immunology
26
The categories of this paper are: biochemistry
3
The categories of this paper are: evolutionary
12
The categories of this paper are: behavior
28
The categories of this paper are: communication
14
The categories of this paper are: biophysics
15
The categories of this paper are: developmental
17
The categories of this paper are: molecular
20
The categories of this paper are: pharmacology
29
The categories of this paper are: education
7
The categories of this paper are: ecology
16
The categories of this paper are: microbiology
5
The categories of this paper are: cell
27
The categories of this paper are: pathology
19
The categories of this paper are: epidemiology
25
The categories of this paper are: bioengineering