Exploratory workbook to perform network analysis on proteomics data from scratch (not using dedicated bioinformatics packages for biological network analysis), using edges defined by the STRING database.
This repository contains nothing too complex and is a learning exercise.
The proteomic data is derived from the raw DIA data files in Project PXD047236 on PRIDE then searched in DIA-NN using an in-silico generated spectral library based on the full human proteome of canonical protein sequences downloaded from the UniProt 2023_04 release.
-
Xie, H., Zhang, Y., Zhu, Z. et al. Plasma Proteomic Analysis Based on 4D-DIA Evaluates the Clinical Response to Imrecoxib in the Early Treatment of Osteoarthritis. Rheumatol Ther 11, 269–283 (2024). https://doi.org/10.1007/s40744-023-00636-z
-
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131. PMID: 30476243; PMCID: PMC6323986.