Differential kinase activity inference from phosphosproteomics data
Project description
Kinase activity inference from phosphosproteomics data based on substrate sequence specificity
Current version:
0.7.1
Research paper: https://doi.org/10.1101/2024.03.22.586304
Benchmark repository: https://github.com/alussana/phosx-benchmark
Overview
PhosX infers differential kinase activities from phosphoproteomics data without requiring any prior knowledge database of kinase-phosphosite associations. PhosX assigns the detected phosphopeptides to potential upstream kinases based on experimentally determined substrate sequence specificities, and it tests the enrichment of a kinase's potential substrates in the extremes of a ranked list of phosphopeptides using a Kolmogorov-Smirnov-like statistic. A p value for this statistic is extracted empirically by random permutations of the phosphosite ranks.
Installation
From PyPI
pip install phosx
From source (requires Poetry)
poetry build
pip install dist/*.whl
Usage
Run PhosX with default parameters on an example dataset, using up to 8 cores, and redirecting the output table to kinase_activities.tsv
:
phosx -c 8 tests/seqrnk/koksal2018_log2.fold.change.8min.seqrnk > kinase_activities.tsv
See the full list of command line options with phosx -h
.
Alongside the main program, this package also installs make-seqrnk
. This utily can be used to easily generate a seqrnk file, which is used as input by PhosX, given a list of phosphosites, each one identified by a UniProtAC and residue coordinate. make-seqrnk
will query the UniProt database to fetch the appropriate subsequences and build the seqrnk file. Run make-seqrnk -h
for more details, or see an example with:
cat tests/p_list/15_3.tsv | make-seqrnk > 15_3.seqrnk
Cite
BibTeX:
@article{Lussana2024,
title = {PhosX: data-driven kinase activity inference from phosphoproteomics experiments},
url = {http://dx.doi.org/10.1101/2024.03.22.586304},
DOI = {10.1101/2024.03.22.586304},
publisher = {Cold Spring Harbor Laboratory},
author = {Lussana, Alessandro and Petsalaki, Evangelia},
year = {2024},
month = mar
}
Project details
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