Below you will find pages that utilize the taxonomy term “frontiers”
Blog
Reconstructed Salmonella Signaling Network Visualized and Colored
After fold changes were obtained and HGNC names were found for each phosphopeptide, these were used to construct Salmonella signaling network using PCSF and then with the nodes that PCSF found as well, we generated a matrix which has node in the rows and time points in the columns and each cell shows the presence of corresponding protein under the corresponding time point(s).
The matrix has 658 nodes (proteins) and 4 time points as indicated before: 2 min, 5 min, 10 min and 20 min.
Blog
Salmonella Data Preprocessing for PCSF Algorithm
This post describes data preprocessing in Salmonella project for Prize-Collecting Steiner Forest Problem (PCSF) algorithm.
Salmonella data taken from Table S6 in Phosphoproteomic Analysis of Salmonella-Infected Cells Identifies Key Kinase Regulators and SopB-Dependent Host Phosphorylation Events by Rogers, LD et al. has been converted to tab delimited TXT file from its original XLS file for easy reading in Python.
The data should be separated into time points files (2, 5, 10 and 20 minutes) each of which will contain corresponding phophoproteins and their fold changes.